PaperBLAST

PaperBLAST Hits for VIMSS92138 hypothetical protein (87 a.a., MKTKLNELLE...)

Show query sequence

>VIMSS92138 hypothetical protein
MKTKLNELLEFPTPFTYKVMGQALPELVDQVVEVVQRHAPGDYTPTVKPSSKGNYHSVSI
TINATHIEQVETLYEELGKIDIVRMVL

Running BLASTp...

Found 12 similar proteins in the literature:

YbeD / b0631 DUF493 domain-containing protein YbeD from Escherichia coli K-12 substr. MG1655 (see 4 papers)
ybeD / PDB|1RWU UPF0250 protein ybeD from Escherichia coli K12 (see paper)
ECs0669 hypothetical protein from Escherichia coli O157:H7 str. Sakai
NP_415164 DUF493 domain-containing protein YbeD from Escherichia coli str. K-12 substr. MG1655
b0631 hypothetical protein from Escherichia coli str. K-12 substr. MG1655
c0721 Hypothetical protein ybeD from Escherichia coli CFT073
100% identity, 100% coverage

• Transcriptomic analysis of Escherichia coli O157:H7 and K-12 cultures exposed to inorganic and organic acids in stationary phase reveals acidulant- and strain-specific acid tolerance responses
  King, Applied and environmental microbiology 2010
  • “...ENVIRON. MICROBIOL. ECs4157 ECs4461 ECs4697 ECs4058 ECs0430 ECs0669 ECs2049 ECs2558 ECs3033 ECs4111 ECs4197 ECs4416 ECs5464 b3292 b3585 b3755 b3179 b0380 b0631...”
• Structural similarity of YbeD protein from Escherichia coli to allosteric regulatory domains.
  Kozlov, Journal of bacteriology 2004
  • GeneRIF: YbeD shows striking structural homology to the regulatory domain from d-3-phosphoglycerate dehydrogenase, hinting at a role in the allosteric regulation of lipoic acid biosynthesis or the glycine cleavage system.
• A new regulatory mechanism for bacterial lipoic acid synthesis
  Zhang, MicrobiologyOpen 2015
  • “...Position 1 Score Enterobacter sp. 638 ybeD Ent638_1166 AAGTGTGATTTCCATCCCCATA 90 4.4 Escherichia coli MG1655 ybeD b0631 AAGTGTAATTTCCGTCCCCATA 94 3.6 Cistrobacter koseri ybeD CKO_02527 AAGTGTGATTTCCATCCCCATA 91 4.4 Klebsiella pneumonia ybeD KPN_00663 AAGTGTGATTTCCATCCCCATA 97 4.4 Salmonella typhimurium LT2 ybeD STM0636 AGTTGTTATTTTTTTTACGTAA AAGTGTGATTTTCGTCCCCATA 35 93 3.9 4.2 Yersinia pestis...”
• Transcriptomic analysis of Escherichia coli O157:H7 and K-12 cultures exposed to inorganic and organic acids in stationary phase reveals acidulant- and strain-specific acid tolerance responses
  King, Applied and environmental microbiology 2010
  • “...ECs4197 ECs4416 ECs5464 b3292 b3585 b3755 b3179 b0380 b0631 b1445 b1848 b2141 b3238 b3346 b3536 b4537 Translation, ribosomal structure and biogenesis Poorly...”
• Sxy induces a CRP-S regulon in Escherichia coli
  Sinha, Journal of bacteriology 2009
  • “...b1322 b2592 b2614 b0014 b2699 b0966 b3686 b3687 b3635 b4140 b0631 bssS ycjF clpB grpE dnaK recA hspQ ibpB ibpA mutM fxsA ybeD 4.48 4.64 5.43 5.47 5.54 5.81...”
• Differential gene expression for investigation of Escherichia coli biofilm inhibition by plant extract ursolic acid
  Ren, Applied and environmental microbiology 2005
  • “...b0594 b4140 b1594 b1739 b3498 b1194 b1321 b1566 b1760 b0141 b2674 b0631 b1322 b2157 b3292 b3525 b4367 b3399 1.4 1.1 1.4 1.3 1.8 1.4 1.6 1.3 1.5 1.6 1.4 1.5 1.0...”
• Interfering with different steps of protein synthesis explored by transcriptional profiling of Escherichia coli K-12
  Sabina, Journal of bacteriology 2003
  • “...b3321 b3308 b3304 b3616 b3339 b2155 b3829 b3317 b3296 b2913 b0631 b2416 b3305 b3303 b1043 b3509 0.03 0.11 0.13 0.16 0.17 0.18 0.21 0.21 0.21 0.22 0.23 0.23 0.24...”
• Establishment of a Reverse Genetics System for SARS-CoV-2 Using Circular Polymerase Extension Reaction
  Torii, 2020

STM14_0743 DUF493 family protein YbeD from Salmonella enterica subsp. enterica serovar Typhimurium str. 14028S
STM0636 putative cytoplasmic protein from Salmonella typhimurium LT2
98% identity, 100% coverage

• Inorganic Polyphosphate Is Essential for Salmonella Typhimurium Virulence and Survival in Dictyostelium discoideum
  Varas, Frontiers in cellular and infection microbiology 2018
  • “...protein STM14_0529 STM0447 tig Trigger factor STM14_0564 STM0479 Putative transposase STM14_0693 STM0595 entC Isochorismate synthase STM14_0743 STM0636 ybeD Hypothetical protein STM14_0806 STM0691 Tricarballylate dehydrogenase STM14_0815 STM0698 pgm Phosphoglucomutase STM14_1013 STM0863 dacC D-alanyl-D-alanine carboxypeptidase fraction C STM14_1056 STM0939 ybjD Hypothetical protein STM14_1106 STM0978 aroA 3-phosphoshikimate 1-carboxyvinyltransferase STM14_1259...”
• Inorganic Polyphosphate Is Essential for Salmonella Typhimurium Virulence and Survival in Dictyostelium discoideum
  Varas, Frontiers in cellular and infection microbiology 2018
  • “...STM14_0529 STM0447 tig Trigger factor STM14_0564 STM0479 Putative transposase STM14_0693 STM0595 entC Isochorismate synthase STM14_0743 STM0636 ybeD Hypothetical protein STM14_0806 STM0691 Tricarballylate dehydrogenase STM14_0815 STM0698 pgm Phosphoglucomutase STM14_1013 STM0863 dacC D-alanyl-D-alanine carboxypeptidase fraction C STM14_1056 STM0939 ybjD Hypothetical protein STM14_1106 STM0978 aroA 3-phosphoshikimate 1-carboxyvinyltransferase STM14_1259 STM1109...”
• A new regulatory mechanism for bacterial lipoic acid synthesis
  Zhang, MicrobiologyOpen 2015
  • “...CKO_02527 AAGTGTGATTTCCATCCCCATA 91 4.4 Klebsiella pneumonia ybeD KPN_00663 AAGTGTGATTTCCATCCCCATA 97 4.4 Salmonella typhimurium LT2 ybeD STM0636 AGTTGTTATTTTTTTTACGTAA AAGTGTGATTTTCGTCCCCATA 35 93 3.9 4.2 Yersinia pestis ybeD y1174 TATTGTGATTAATCTTATATTG 146 4.2 Shewanella baltica lipB Sba_3281 AAATGTGATCTGTCTTACATTT 74 5.2 S. halifaxensis lipB ShaI_3240 AAATGTGATCCGTATTACATTT 76 5.2 S. loihica lipB...”

KPN_00663 hypothetical protein from Klebsiella pneumoniae subsp. pneumoniae MGH 78578
97% identity, 100% coverage

• A new regulatory mechanism for bacterial lipoic acid synthesis
  Zhang, MicrobiologyOpen 2015
  • “...ybeD b0631 AAGTGTAATTTCCGTCCCCATA 94 3.6 Cistrobacter koseri ybeD CKO_02527 AAGTGTGATTTCCATCCCCATA 91 4.4 Klebsiella pneumonia ybeD KPN_00663 AAGTGTGATTTCCATCCCCATA 97 4.4 Salmonella typhimurium LT2 ybeD STM0636 AGTTGTTATTTTTTTTACGTAA AAGTGTGATTTTCGTCCCCATA 35 93 3.9 4.2 Yersinia pestis ybeD y1174 TATTGTGATTAATCTTATATTG 146 4.2 Shewanella baltica lipB Sba_3281 AAATGTGATCTGTCTTACATTT 74 5.2 S. halifaxensis...”

Ent638_1166 hypothetical protein from Enterobacter sp. 638
95% identity, 100% coverage

• A new regulatory mechanism for bacterial lipoic acid synthesis
  Zhang, MicrobiologyOpen 2015
  • “...species amongst -proteobacteria Organisms Gene Loci CRP site Position 1 Score Enterobacter sp. 638 ybeD Ent638_1166 AAGTGTGATTTCCATCCCCATA 90 4.4 Escherichia coli MG1655 ybeD b0631 AAGTGTAATTTCCGTCCCCATA 94 3.6 Cistrobacter koseri ybeD CKO_02527 AAGTGTGATTTCCATCCCCATA 91 4.4 Klebsiella pneumonia ybeD KPN_00663 AAGTGTGATTTCCATCCCCATA 97 4.4 Salmonella typhimurium LT2 ybeD STM0636...”

y1174 hypothetical protein from Yersinia pestis KIM
YPTB1093 hypothetical protein from Yersinia pseudotuberculosis IP 32953
84% identity, 100% coverage

• A new regulatory mechanism for bacterial lipoic acid synthesis
  Zhang, MicrobiologyOpen 2015
  • “...4.4 Salmonella typhimurium LT2 ybeD STM0636 AGTTGTTATTTTTTTTACGTAA AAGTGTGATTTTCGTCCCCATA 35 93 3.9 4.2 Yersinia pestis ybeD y1174 TATTGTGATTAATCTTATATTG 146 4.2 Shewanella baltica lipB Sba_3281 AAATGTGATCTGTCTTACATTT 74 5.2 S. halifaxensis lipB ShaI_3240 AAATGTGATCCGTATTACATTT 76 5.2 S. loihica lipB Shew_2941 AAATGTGATCTACCTTACATTT 70 5.3 S. oneidensis lipB SO1162 AAGTGTGATCTATCTTACATTT 68...”
• IscR is essential for yersinia pseudotuberculosis type III secretion and virulence
  Miller, PLoS pathogens 2014
  • “...Proteins(9) YPTB0391 putative exported protein 2.1 YPTB0449 hypothetical protein 3.3 YPTB0458 putative exported protein 2.2 YPTB1093 hypothetical protein 3.6 YPTB1571 hypothetical protein 2.1 YPTB2255 putative exported protein 2.3 YPTB2277 hypothetical protein 2.6 YPTB2496 hypothetical protein 2.8 YPTB3109 hypothetical protein 4.1 a ORF IDs are derived from...”

VF_0744 DUF493 family protein YbeD from Aliivibrio fischeri ES114
VF_0744 hypothetical protein from Vibrio fischeri ES114
71% identity, 94% coverage

• Characterizing the host and symbiont proteomes in the association between the Bobtail squid, Euprymna scolopes, and the bacterium, Vibrio fischeri
  Schleicher, PloS one 2011
  • “...hydroperoxide reductase, C22 10.54 994 6 59711657 VF_1050 - hypothetical protein 9.35 179 7 59711351 VF_0744 ybeD hypothetical protein 7.94 194 8 59712374 VF_1767 cspD DNA replication inhibitor 7.66 309 9 59714005 VF_A0822 - hypothetical protein 7.55 101 10 59711823 VF_1216 infC protein chain initiation factor...”

SO1163 conserved hypothetical protein from Shewanella oneidensis MR-1
56% identity, 99% coverage

• A new regulatory mechanism for bacterial lipoic acid synthesis
  Zhang, MicrobiologyOpen 2015
  • “...species from the RegPrecise database (Novichkov etal. 2010a ). We noted that the ybeD ( SO1163 ) gene is constantly present upstream of the lipB gene (Fig. 2 ), and YbeD protein of E. coli origin exhibits a striking structural homology to the allosteric regulatory domain...”
• Stress responses of shewanella
  Yin, International journal of microbiology 2011
  • “...76 48 GTTGAAAAGAATTGATTTGCCCCAAGATA 12.8 SO1794 clpP ATP-dependent Clp protease, proteolytic subunit 83 55 CTTGACTTGATTAGCAGTTCGCCATTTAT 12.8 SO1163 conserved hypothetical protein 60 31 CTTGAATCGGGTATAATCGCCACCATATAG 12.7 SO3863 modA molybdenum ABC transporter, periplasmic molybdenum-binding protein 206 177 CTTGAGTAAATGTTATTGTCCCCGATCAAT 12.3 SO1196 rrmJ ribosomal RNA large subunit methyltransferase J 65 36 GTTGAAAAACCGCTATTCTACCCTTATATA...”

NGO0791 hypothetical protein from Neisseria gonorrhoeae FA 1090
39% identity, 88% coverage

• Global Network Analysis of Neisseria gonorrhoeae Identifies Coordination between Pathways, Processes, and Regulators Expressed during Human Infection
  McClure, mSystems 2020
  • “...hypothetical proteins. These hypothetical proteins include NGO0672, NGO1301, NGO1861, NGO2068 (a putative membrane protein), NGO1518, NGO0791 (containing a domain with lipoic acid-binding regulatory protein homology), and NGO0350 (containing a domain with hemolysin binding homology). Degree and betweenness values for all genes in the network are shown...”
• RpoH mediates the expression of some, but not all, genes induced in Neisseria gonorrhoeae adherent to epithelial cells
  Du, Infection and immunity 2006
  • “...NGO1363 NGO1989 NGO0340 NGO0238 NGO1210 NGO0634 NGO0372 NGO0791 NGO1927 NGO0635 NGO1083 NGO0633 NGO1988 NGO0234 NGO0721 NGO1366 NGO1291 NGO0199 NGO1515 NGO1493...”

NMB1218 hypothetical protein from Neisseria meningitidis MC58
38% identity, 88% coverage

• Laminin receptor initiates bacterial contact with the blood brain barrier in experimental meningitis models
  Orihuela, The Journal of clinical investigation 2009
  • “...confirmed by PCR analysis. The pilQ gene (NMB1218) and its flanking sequence were amplified using the primers PilQF1 (5-GCCGTCTGAAACAGCTGCCGACAGATGC-3) and...”

BCAL0706 hypothetical protein from Burkholderia cenocepacia J2315
37% identity, 85% coverage

• Burkholderia cenocepacia differential gene expression during host-pathogen interactions and adaptation to the host environment
  O'Grady, Frontiers in cellular and infection microbiology 2011
  • “...(HAP3) 3.20 BCAL0621 Putative cyclic-di-GMP signaling protein 1.56 BCAL0705 Putative d -amino acid aminotransferase 1.55 BCAL0706 Conserved hypothetical protein 1.75 BCAL0744 Appr-1-p processing enzyme family protein 1.74 BCAL0771 Non-heme chloroperoxidase 1.82 BCAL0808 P-loop ATPase protein family protein 1.88 BCAL0812 Sigma-54 modulation protein 1.91 BCAL0813 Putative RNA...”

PLES_09781 hypothetical protein from Pseudomonas aeruginosa LESB58
B7V8B5 UPF0250 protein PLES_09781 from Pseudomonas aeruginosa (strain LESB58)
PA3998 hypothetical protein from Pseudomonas aeruginosa PAO1
40% identity, 85% coverage

• Proteomic profiling spotlights the molecular targets and the impact of the natural antivirulent umbelliferone on stress response, virulence factors, and the quorum sensing network of Pseudomonas aeruginosa
  Kasthuri, Frontiers in cellular and infection microbiology 2022
  • “...ATP-binding protein AraG 0.01 1.96 B7UVT6 Probable cytosol aminopeptidase PepA 0.02 2.71 B7V8B5 UPF0250 protein PLES_09781 0.02 2.31 Q8XWT3 Pantothenate synthetase PanC 0.02 1.79 Q1I2H5 tRNA modification GTPase MnmE 0.02 4.14 P47203 Cell division protein FtsA 0.02 1.24 Q88FY7 Porin-like protein NicP 0.02 6.69 Q9HTB6 GDP-6-deoxy-D-mannose...”
• Proteomic profiling spotlights the molecular targets and the impact of the natural antivirulent umbelliferone on stress response, virulence factors, and the quorum sensing network of Pseudomonas aeruginosa
  Kasthuri, Frontiers in cellular and infection microbiology 2022
  • “...Q8XVS2 Arabinose import ATP-binding protein AraG 0.01 1.96 B7UVT6 Probable cytosol aminopeptidase PepA 0.02 2.71 B7V8B5 UPF0250 protein PLES_09781 0.02 2.31 Q8XWT3 Pantothenate synthetase PanC 0.02 1.79 Q1I2H5 tRNA modification GTPase MnmE 0.02 4.14 P47203 Cell division protein FtsA 0.02 1.24 Q88FY7 Porin-like protein NicP 0.02...”
• Bacterial fitness in chronic wounds appears to be mediated by the capacity for high-density growth, not virulence or biofilm functions
  Morgan, PLoS pathogens 2019
  • “...0 0.000 nt PA1929 - 165 0 0.000 nt PA3263 - 162 0 0.000 nt PA3998 - 162 0 0.000 nt PA0025 aroE 160 0 0.000 nt PA1479 ccmE 146 0 0.000 nt PA4600 nfxB 129 0 0.000 nt PA5288 glnK 122 0 0.000 nt PA5322...”

A1S_2705 hypothetical protein from Acinetobacter baumannii ATCC 17978
33% identity, 86% coverage

• Whole transcriptome analysis of Acinetobacter baumannii assessed by RNA-sequencing reveals different mRNA expression profiles in biofilm compared to planktonic cells
  Rumbo-Feal, PloS one 2013
  • “...A1S_2534 sulfate transport protein 21.12 from zero to 24.66 ** A1S_2696 hypothetical protein 1.35 0.20 A1S_2705 hypothetical protein 0.21 0.09 A1S_2718 succinyl-CoA synthetase subunit beta 1.14 7.65 A1S_2719 succinyl-CoA synthetase subunit alpha 1.07 5.76 A1S_2753 hypothetical protein 1.66 3.36 A1S_2840 outer membrane protein A 0.60 0.74...”

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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.