PaperBLAST

PaperBLAST Hits for 87 a.a. (MEPIFIIGII...)

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>87 a.a. (MEPIFIIGII...)
MEPIFIIGIILGLVILLFLSGSAAKPLKWIGITAVKFVAGALLLVCVNMFGGSLGIHVPI
NLVTTAISGILGIPGIAALVVIKQFII

Running BLASTp...

Found 5 similar proteins in the literature:

BOFA_BACSU / P24282 Sigma-K factor-processing regulatory protein BofA; Bypass-of-forespore protein A from Bacillus subtilis (strain 168) (see 3 papers)
NP_387904 inhibitor of the pro-sigma(K) processing machinery from Bacillus subtilis subsp. subtilis str. 168
BSU00230 inhibitor of the pro-sigma(K) processing machinery from Bacillus subtilis subsp. subtilis str. 168
100% identity, 100% coverage

• function: Involved in the mediation of the intercompartmental coupling of pro-sigma K processing to events in the forespore. Inhibits SpoIVFB- processing activity until a signal has been received from the forespore. Could inhibit SpoIVFB metalloprotease activity by coordinating a zinc in the SpoIVFB active site, preventing access of a water molecule and the sequence of pro-sigma K, which are necessary for peptide bond hydrolysis to produce sigma-K.
  subunit: Forms a complex with SpoIVFA and SpoIVFB localized in the mother cell membrane surrounding the forespore.
• gerT, a newly discovered germination gene under the control of the sporulation transcription factor sigmaK in Bacillus subtilis.
  Ferguson, Journal of bacteriology 2007
  • GeneRIF: The gerT gene is induced late in sporulation under the positive control of the transcription factor sigma(K).
• Prediction of the functional class of metal-binding proteins from sequence derived physicochemical properties by support vector machine approach
  Lin, BMC bioinformatics 2006
  • “...+ P54657 + Q56X52 + O42720 - P24059 + P56200 - Q59660 - O67672 + P24282 - P80479 + Q6F4C6 + O68557 + P26902 + P80509 - Q7Z2C4 + O75448 + P28875 + P81040 + Q80874 + O81916 + P31032 + P81242 - Q8GNT2 + P03697...”
• The program of gene transcription for a single differentiating cell type during sporulation in Bacillus subtilis
  Eichenberger, PLoS biology 2004
  • “...the gene products discussed in this paper are E (P06222), G (P19940), K (P12254), BofA (P24282), CodY (P39779), GerE (P11470), GerR (O34549), RacA (P45870), Spo0A (P06534), SpoIIID (P15281), SpoIVFA (P26936), and SpoIVFB (P26937). The GenBank ( http://www.ncbi.nlm.nih.gov/Genbank ) accession numbers for the genes discussed in this...”
• The Multiomics Response of Bacillus subtilis to Simultaneous Genetic and Environmental Perturbations
  Liu, Microorganisms 2023
  • “...upregulated genes between t2 and t1 ( Figure 5 A), for the biosynthesis of purine (bsu00230) and pyrimidine (bsu00240) and many amino acids metabolism (bsu00220:arginine biosynthesis). Specifically, the identities of amino acids having upregulated expression were different between WT and MT1. Expectedly, the functional groups enriched...”
• Time-Course Transcriptome Analysis of Bacillus subtilis DB104 during Growth
  Jun, Microorganisms 2023
  • “...amino acids 0 29 0 0 0 bsu02020 Two-component system 28 0 0 0 0 bsu00230 Purine metabolism 17 0 10 0 0 bsu00650 Butanoate metabolism 7 6 6 0 0 bsu00020 Citrate cycle (TCA cycle) 8 10 0 0 0 microorganisms-11-01928-t004_Table 4 Table 4 Transcripts...”
• Assessing in silico the recruitment and functional spectrum of bacterial enzymes from secondary metabolism
  Veprinskiy, BMC evolutionary biology 2017
  • “...1/0 bsu00970 Aminoacyl-tRNA biosynthesis 1/0 bsu01200 Carbon metabolism 1/0 bsu00770 Pantothenate and CoA biosynthesis 1/0 bsu00230 Purine metabolism 1/1 bsu01230 Biosynthesis of amino acids bsu:BSU00650 yabS; hypothetical protein; K07114 Ca-activated chloride channel homolog P bsu:BSU00660 yabT; serine/threonine protein kinase (EC 2.7.11.1) P bsu:BSU00670 tilS; tRNA(ile)-lysidine synthase;...”
  • “...Two-component system 1/0 bsu00790 Folate biosynthesis 1/0 bsu02030 Bacterial chemotaxis 1/0 bsu00240 Pyrimidine metabolism 1/0 bsu00230 Purine metabolism 1/0 bsu00340 Histidine metabolism 1/0 bsu00360 Phenylalanine metabolism 1/0 bsu00130 Ubiquinone and other terpenoid-quinone biosynthesis 1/0 bsu00350 Tyrosine metabolism P S bsu:BSU22600 aroE; 3-phosphoshikimate 1-carboxyvinyltransferase (EC 2.5.1.19) P...”
• Changes in the Acetylome and Succinylome of Bacillus subtilis in Response to Carbon Source
  Kosono, PloS one 2015
  • “...and isoleucine biosynthesis 14 3.0 1.07E-04 2.9 8.97E03 bsu03010 Ribosome 40 8.5 7.15E-10 2.5 6.00E08 bsu00230 Purine metabolism 33 7.0 1.17E-05 2.0 9.81E04 In the citrate condition bsu00970 Aminoacyl-tRNA biosynthesis 17 3.3 1.29E-04 2.5 0.0112 bsu00020 Citrate cycle (TCA cycle) 16 3.1 3.22E-04 2.5 0.0277 bsu03010...”
• The program of gene transcription for a single differentiating cell type during sporulation in Bacillus subtilis
  Eichenberger, PLoS biology 2004
  • “...argC (BSU11190), argJ (BSU11200), asnO (BSU10790), azlB (BSU26720), azlC (BSU26710), azlD (BSU26700), bnrQ (BSU26690), bofA (BSU00230), cotA (BSU06300), cotD (BSU22200), cotE (BSU17030), cotF (BSU40530), cotH (BSU36060), cotM (BSU17970), cotT (BSU12090), cotV (BSU11780), cotW (BSU11770), ctpB/yvjB (BSU35240), cwlC (BSU17410), cwlH (BSU25710), cwlJ (BSU02600), cypA (BSU26740), cysC (BSU15600),...”

bofA / GB|BAA05259.1 sigma-K factor processing regulatory protein BofA from Bacillus subtilis (see 8 papers)
99% identity, 100% coverage

BPUM_0520 possible sigma-K factor-processing regulatory protein BofA from Bacillus pumilus SAFR-032
64% identity, 100% coverage

• Bacillus pumilus SAFR-032 Genome Revisited: Sequence Update and Re-Annotation
  Stepanov, PloS one 2016 (no snippet)

BC0028 SigmaK-factor processing regulatory protein BofA from Bacillus cereus ATCC 14579
BTF1_26160 pro-sigmaK processing inhibitor BofA family protein from Bacillus thuringiensis HD-789
45% identity, 88% coverage

• Multi-locus sequence typing and virulence profile in Bacillus cereus sensu lato strains isolated from dairy products
  Bianco, Italian journal of food safety 2020
  • “...Caciocavallo ST-142 complex 4 + + + + + + + + + + - BC0028 Caciocavallo 59 + - + + + + + + + + - BC0029 Caciocavallo 2041* + + + + + + + + + + - BC0030 Mozzarella 369...”
• NagR_Bt Is a Pleiotropic and Dual Transcriptional Regulator in Bacillus thuringiensis
  Cao, Frontiers in microbiology 2018
  • “...8.62 NS NT BTF1_24430 chbB PTS system, lichenan-specific IIB component 249 agttgtctagttatgc 9.2 NS NT BTF1_26160 bofA SigmaK-factor processing regulatory protein BofA 39 atacaaatagatgtat 7.19 NS NT a The BTF1 number of genes are the open reading frames based on the genome annotation of B. thuringiensis...”
  • “...O: pepT , BTF1_19055; P: wall-associated protein, BTF1_23845; Q: chbB , BTF1_24430; R: bofA , BTF1_26160. NagR Bt activates the expression of some genes directly The gene encoding a hypothetical protein (BTF1_19025) and the pgi (glucose-6-phosphate isomerase, BTF1_23020) gene both possess a predicted dre site, and...”

CPE0049 hypothetical protein from Clostridium perfringens str. 13
40% identity, 88% coverage

• Global regulation of gene expression in response to cysteine availability in Clostridium perfringens
  André, BMC microbiology 2010
  • “...cpe2151 Mercure-copper binding protein 5.1 < 1E-05 cpe1371 Na + -dependent symporter 3.3 0.009 5 cpe0049 Membrane protein 3.02 < 1E-05 cpe2456 Membrane protein 2.84 1E-05 cpe0554 Protein with signal sequence 2.74 0.0002 cpe0383 Holin-like protein 2.6 0.004 cpe2595 Na + /H + antiporter 0.34 <...”

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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.