PaperBLAST
PaperBLAST Hits for BRENDA::Q6GH41 (61 a.a., MPIVNVKLLE...)
Show query sequence
>BRENDA::Q6GH41
MPIVNVKLLEGRSDEQLKNLVSEVTDAVEKTTGANRQAIHVVIEEMKPNHYGVAGVRKSD
Q
Running BLASTp...
Found 27 similar proteins in the literature:
NWMN_1275 4-oxalocrotonate tautomerase from Staphylococcus aureus subsp. aureus str. Newman
SAS044 4-oxalocrotonate tautomerase from Staphylococcus aureus subsp. aureus N315
SAR1376 putative 4-oxalocrotonate tautomerase from Staphylococcus aureus subsp. aureus MRSA252
100% identity, 98% coverage
- Induction of virulence gene expression in Staphylococcus aureus by pulmonary surfactant
Ishii, Infection and immunity 2014 - “...NWMN_0902 NWMN_0909 NWMN_1059 NWMN_1106 NWMN_1196 NWMN_1275 NWMN_1554 NWMN_1716 NWMN_1745 NWMN_1776 NWMN_1861 NWMN_1898 NWMN_2074 NWMN_2188 NWMN_2189 NWMN_2320...”
- Identification and characterization of mutations responsible for the β-lactam resistance in oxacillin-susceptible mecA-positive Staphylococcus aureus
Boonsiri, Scientific reports 2020 - “...SA0499 and rpoB , sgtB and SA1692, E8M03_00305 and hsdR , SA2092 and ssaA2 , SAS044 and SA1196, norB and ebhA , tnp and proP , and SA1447 and alaS , respectively. These results clearly demonstrated that mutations responsible for oxacillin resistance in the OS-MRSA-derived mutants...”
- Analysis of the matrix-assisted laser desorption ionization-time of flight mass spectrum of Staphylococcus aureus identifies mutations that allow differentiation of the main clonal lineages
Josten, Journal of clinical microbiology 2013 - “...SAS049 rpmF (SAS033) rpmD (SA2030) SA1452 graC (SAS044) SA2039 rpsP (SA1081) Primer sequence SAS078for SAS078rev SAR1012for SAR1012rev SA0772for SA0772rev...”
- “...(SA2030) rpmD (SA2030) SA1452 SA1452 SA1452 SA1452 graC (SAS044) graC (SAS044) graC (SAS044) graC (SAS044) SA0772 rpmC (SA2039) rpmC (SA2039) rpmC (SA2039) rpsT...”
- Genetic changes associated with glycopeptide resistance in Staphylococcus aureus: predominance of amino acid substitutions in YvqF/VraSR
Kato, The Journal of antimicrobial chemotherapy 2010 - “...GTAAAGCGGTGCATAATACAG 3645 msrR region SA1193-SA1195, SAS044 fmtC, msrA, msrR and SAS044 SA1193-95F SA1193-95R TGTGCAGGCAAATTGCTTGG TTCAATACAAGAAACACTCGCA 5513...”
- Characterizing the effect of the Staphylococcus aureus virulence factor regulator, SarA, on log-phase mRNA half-lives
Roberts, Journal of bacteriology 2006 - “...5 5 5 5 5 5 SA1075 SA1234 SA2312 SAS044 SA1305 SA2023 SA0353 SA1913 SA0182 SA0529 SA1528 Acyl carrier protein Major cold shock protein CspA D-Specific...”
- Overexpression of genes of the cell wall stimulon in clinical isolates of Staphylococcus aureus exhibiting vancomycin-intermediate- S. aureus-type resistance to vancomycin
McAleese, Journal of bacteriology 2006 - “...SA0820 SA0937 glpQ SA0969 SA1236 SA0341 SA2146 SA2297 SA2481 SAS044 SA0166 csbD yvqF tcaA dmp1 spsA spsB SA0825 SA0826 SA0204 SA0022 SA0918 purC SA0921 SA1549...”
- Transcriptomic and functional analysis of an autolysis-deficient, teicoplanin-resistant derivative of methicillin-resistant Staphylococcus aureus
Renzoni, Antimicrobial agents and chemotherapy 2006 - “...1.17 1.04 0.97 0.1 0.05 0.04 NS NS NS SA0743 SAS044 SA1318 SA1337 SA1339 SAS030 SA0016 SA1724 SA0918 SA0926 SA0916 graB graC graD graE malR graF purA purB purC...”
- DNA microarray-based identification of genes associated with glycopeptide resistance in Staphylococcus aureus
Cui, Antimicrobial agents and chemotherapy 2005 - “...IDd SA0614 SA0615 SA0639 SA0641 SA0743 SA1194 SA1195 SAS044 SA1225 SA1318 SA1337 SA1339 SA1691 SA1869 SA1872 SA1926 SAS030 Oxacillin Imipenem E-test Agar E-test...”
- The S. aureus 4-oxalocrotonate tautomerase SAR1376 enhances immune responses when fused to several antigens
Diemen, Scientific reports 2017 - “...Publishing Group UK London 5431793 28496136 1421 10.1038/s41598-017-01421-z Article The S . aureus 4-oxalocrotonate tautomerase SAR1376 enhances immune responses when fused to several antigens Diemen Pauline M. van 1 http://orcid.org/0000-0002-9944-5258 Leneghan Darren B. 2 Brian Iona J. 2 Miura Kazutoyo 3 Long Carole A. 3 Milicic...”
- “...to crystallise into multimeric structures have been examined for their scaffolding potential. Of these domains, SAR1376, a 62 amino acid member of the 4-oxalocrotonate tautomerase (4-OT) family, was pro-immunogenic in mice when fused to a range of pathogen antigens from both S . aureus and P...”
- The Scottish Structural Proteomics Facility: targets, methods and outputs
Oke, Journal of structural and functional genomics 2010 - “...1 Amenable A 2X7I SAR0482 Se-SAD MRSA Orn/Lys/Arg decarboxylase family protein 2 High-scoring A 2X3L SAR1376 Zn MRSA Putative 4-oxalocrotonate tautomerase 5 Amenable 2X4K PPFK (Q6GIU3) MR MRSA Putative phosphofructokinase 1 Amenable A 2JG5 TAG (Q6GG41) Zn-SAD MRSA DNA-3-methyladenine glycosylase I 1 High-scoring A 2JG6 SPT...”
Q6GH41 2-hydroxymuconate tautomerase (EC 5.3.2.6) from Staphylococcus aureus (see paper)
SAUSA300_1258 4-oxalocrotonate tautomerase from Staphylococcus aureus subsp. aureus USA300_FPR3757
P99132 Probable tautomerase SA1195.1 from Staphylococcus aureus (strain N315)
100% identity, 100% coverage
A0A133Q308 Tautomerase from Staphylococcus lugdunensis
EQ812_07575 2-hydroxymuconate tautomerase from Staphylococcus lugdunensis
85% identity, 100% coverage
SE1045 4-oxalocrotonate tautomerase from Staphylococcus epidermidis ATCC 12228
82% identity, 95% coverage
Q8CPB7 Probable tautomerase SE_1045 from Staphylococcus epidermidis (strain ATCC 12228 / FDA PCI 1200)
82% identity, 100% coverage
BAGQ_3790 2-hydroxymuconate tautomerase from Bacillus velezensis
62% identity, 97% coverage
ywhB / P70994 4-oxalocrotonate tautomerase homolog (EC 5.3.2.1) from Bacillus subtilis (strain 168) (see 5 papers)
4OT_BACSU / P70994 2-hydroxymuconate tautomerase; (2Z,4E)-2-hydroxyhexa-2,4-dienedioate keto-enol isomerase; 4-oxalocrotonate tautomerase; 4-OT; EC 5.3.2.6 from Bacillus subtilis (strain 168) (see paper)
62% identity, 97% coverage
- function: Catalyzes both 1,3- and 1,5-keto-enol tautomerization of the diacid 2-hydroxymuconate (2-hydroxy-2,4-hexadienedioate) to produce 2- oxo-4-hexenedioate. This reaction is highly stereoselective and produces a mixture of stereoisomers, where the (3S)-isomer of 2-oxo-4- hexenedioate predominates. Also catalyzes the tautomerization of 2- hydroxymuconate to 2-oxo-3-hexenedioate, however this reaction is slower and occurs after the tautomerization of 2-hydroxymuconate to 2- oxo-4-hexenedioate. Using 2-hydroxy-2,4-pentadienoate, phenylenolpyruvate, (p-hydroxyphenyl)-enolpyruvate and 2-hydroxy-2,4- heptadiene-1,7-dioate, YwhB is a highly efficient 1,3-keto-enol tautomerase, but clearly not a 1,5-keto-enol tautomerase. Tautomerization of the two monoacids 2-hydroxy-2,4-pentadienoate and phenylenolpyruvate produces a mixture of stereoisomers, where the (3R)- isomers predominate.
catalytic activity: (2Z,4E)-2-hydroxyhexa-2,4-dienedioate = (3E)-2-oxohex-3- enedioate (RHEA:33431)
subunit: Homohexamer. - A Novel Gene Cluster Is Involved in the Degradation of Lignin-Derived Monoaromatics in Thermus oshimai JL-2
Chakraborty, Applied and environmental microbiology 2021 (secret)
lp_1712 4-oxalocrotonate tautomerase from Lactobacillus plantarum WCFS1
61% identity, 95% coverage
- Response of Lactobacillus plantarum WCFS1 to the Gram-Negative Pathogen-Associated Quorum Sensing Molecule N-3-Oxododecanoyl Homoserine Lactone
Spangler, Frontiers in microbiology 2019 - “...0.08 TIG_LACPL lp_2118 tig trigger factor, peptidylprolyl isomerase 0.03 0.158 -0.04 1 0.06 0.52 Y1712_LACPL lp_1712 xylH 4-oxalocrotonate tautomerase -0.23 0.41 0.368 0.91 0.71 0.48 RNAseq values represent Log 2 fold change of gene abundance. Proteomic values represent Log 2 fold change of emPAI values. Descriptions...”
- “...those identified from controls. Proteins encoded from genes such as xylH (putative tautomerase EC 5.3.2.6, lp_1712), dltC1 ( D -alanyl carrier protein 1, lp_2017), iolE (inosine dehydratase, lp_3607), fabI (enoyl-ACP reductase, lp_1681), and dak2 (dihydroxyacetone phosphotransferase, lp_0169) are examples of contributors to this increase in abundance....”
2opaA / P70994 Ywhb binary complex with 2-fluoro-p-hydroxycinnamate
61% identity, 97% coverage
- Ligand: 2-fluoro-3-(4-hydroxyphenyl)-2e-propeneoate (2opaA)
BP9_01400 2-hydroxymuconate tautomerase from Bacillus paralicheniformis
60% identity, 98% coverage
- Comprehensive genomic analysis of Bacillus paralicheniformis strain BP9, pan-genomic and genetic basis of biocontrol mechanism
Asif, Computational and structural biotechnology journal 2023 - “...In addition to siderophore and secondary metabolites (bacitracin, fengycin), BP9 might use those predicted proteins (BP9_01400, BP9_03461, BP9_04050, BP9_01404, etc.) to interact with the P. syringae that could result in reduced virulence ( Table 2 ). Overall, more genes are associated with bacterial leaf blight/bacterial blight...”
- “...web blast analysis. Table 2 Gene E/value Disease Exper. Host Site Prior penetration Spore germination BP9_01400 2.02E- 131 Bacterial leaf blight Oryza sativa leaf Reduced virulence Reduced BP9_03461 2.11E- 97 Black rot disease Raphanus sativus leaf Reduced virulence BP9_01402 4.50E- 142 Bacterial leaf blight Oryza sativa...”
Q71WL5 Probable tautomerase LMOf2365_2536 from Listeria monocytogenes serotype 4b (strain F2365)
58% identity, 98% coverage
EF2859 4-oxalocrotonate tautomerase, putative from Enterococcus faecalis V583
47% identity, 95% coverage
praC / C4TP07 4-oxalocrotonate tautomerase (EC 5.3.2.6) from Paenibacillus sp. JJ-1b (see paper)
C4TP07 2-hydroxymuconate tautomerase (EC 5.3.2.6) from Paenibacillus sp. (see paper)
praC / BAH79105.1 4-oxalocrotonate tautomerase from Paenibacillus sp. JJ-1b (see paper)
41% identity, 97% coverage
xylH / Q01468 4-oxalocrotonate tautomerase subunit (EC 5.3.2.6) from Pseudomonas putida (see 4 papers)
4OT1_PSEPU / Q01468 2-hydroxymuconate tautomerase; 4-oxalocrotonate tautomerase; 4-OT; EC 5.3.2.6 from Pseudomonas putida (Arthrobacter siderocapsulatus) (see 2 papers)
Q01468 2-hydroxymuconate tautomerase (EC 5.3.2.6) from Pseudomonas putida (see 3 papers)
xylH / AAA25694.1 4-oxalocrotonate tautomerase from Pseudomonas putida (see paper)
42% identity, 87% coverage
nahJ / BAE92174.1 4-oxalocrotonate tautomerase NahJ from Pseudomonas putida (see 2 papers)
44% identity, 87% coverage
1bjpA / Q01468 Crystal structure of 4-oxalocrotonate tautomerase inactivated by 2- oxo-3-pentynoate at 2.4 angstroms resolution (see paper)
41% identity, 87% coverage
- Ligand: 2-oxo-3-pentenoic acid (1bjpA)
cnbG / Q38M36 2-hydroxymuconate tautomerase (EC 5.3.2.6) from Comamonas testosteroni CNB-1 (see paper)
40% identity, 95% coverage
P67531 Probable tautomerase spr0921 from Streptococcus pneumoniae (strain ATCC BAA-255 / R6)
P67530 Probable tautomerase SP_1017 from Streptococcus pneumoniae serotype 4 (strain ATCC BAA-334 / TIGR4)
SM12261_RS05070 4-oxalocrotonate tautomerase from Streptococcus mitis NCTC 12261
47% identity, 90% coverage
C3KFP9 2-hydroxymuconate tautomerase from Pseudomonas fluorescens
40% identity, 87% coverage
Rmet_1317 4-oxalocrotonate tautomerase family enzyme from Ralstonia metallidurans CH34
KZ686_10015, Rmet_1317 2-hydroxymuconate tautomerase from Cupriavidus cauae
40% identity, 87% coverage
P49172 2-hydroxymuconate tautomerase (EC 5.3.2.6) from Pseudomonas sp. (see paper)
dmpI / CAA43229.1 4-oxalocrotonate from Pseudomonas sp. CF600 (see paper)
38% identity, 87% coverage
NSU_pLA1132 2-hydroxymuconate tautomerase from Novosphingobium pentaromativorans US6-1
36% identity, 79% coverage
J2M343 Tautomerase from Herbaspirillum sp. CF444
38% identity, 76% coverage
- Introduction of Asymmetry in the Fused 4-Oxalocrotonate Tautomerases
Erwin, Biochemistry 2023 - “...and subunits of a putative heterohexamer 4-OT from Herbaspirillum sp. CF444 (UniProt accession J3DHL6 and J2M343, respectively) were synthesized in the same fashion and the gene products are designated heterohexamer-CF4444OT (hhCF-4OT) and fused-CF4444OT (fCF-4OT). Plasmids were isolated from cell cultures using the Sigma GenElute Plasmid Miniprep...”
- “...The and subunits of a heterohexamer 4-OT from Herbaspirillum sp. CF444 (UniProt accession J3DHL6 and J2M343, respectively) ABBREVIATIONS APS Advanced Photon Source CHM 5-(carboxymethyl)-2-hydroxymuconate DEAE diethylaminoethyl ESI-MS electrospray ionization mass spectrometry fCF-4OT fused-CF4444-oxalocrotonate tautomerase hhCF-4OT heterohexamer CF4444-oxalocrotonate tautomerase fYR-4OT fusedYR5224-oxalocrotonate tautomerase hhYR-4OT heterohexamerYR5224-oxalocrotonate tautomerase HEPES 4-(2-hydroxyethyl)-1-piperazine...”
A2SL37 2-hydroxymuconate tautomerase (EC 5.3.2.6) from Methylibium petroleiphilum (see paper)
40% identity, 77% coverage
Reut_B5693 4-oxalocrotonate tautomerase from Ralstonia eutropha JMP134
32% identity, 95% coverage
HPB8_625 2-hydroxymuconate tautomerase family protein from Helicobacter pylori B8
D7FDC5 Tautomerase from Helicobacter pylori (strain B8)
HP0924 4-oxalocrotonate tautomerase (dmpI) from Helicobacter pylori 26695
36% identity, 81% coverage
- Alteration of the Helicobacter pylori membrane proteome in response to changes in environmental salt concentration
Voss, Proteomics. Clinical applications 2015 - “...2.26 Putative uncharacterized protein HP0467 HPB8_258 * & D7FCA8 heme binding 2.18 Cytochrome c553 HP1227 HPB8_625 D7FDC5 cellular aromatic compound metabolic process 2.15 4-oxalocrotonate tautomerase (DmpI) HP0924 HPB8_829 * D7FDX9 NA 2.1 Modulator of drug activity B (MDA66) HP0630 HPB8_958 * & D7FEA8 NA 2.07 Flagellar...”
- Alteration of the Helicobacter pylori membrane proteome in response to changes in environmental salt concentration
Voss, Proteomics. Clinical applications 2015 - “...Putative uncharacterized protein HP0467 HPB8_258 * & D7FCA8 heme binding 2.18 Cytochrome c553 HP1227 HPB8_625 D7FDC5 cellular aromatic compound metabolic process 2.15 4-oxalocrotonate tautomerase (DmpI) HP0924 HPB8_829 * D7FDX9 NA 2.1 Modulator of drug activity B (MDA66) HP0630 HPB8_958 * & D7FEA8 NA 2.07 Flagellar protein...”
- Delineation of the pH-Responsive Regulon Controlled by the Helicobacter pylori ArsRS Two-Component System
Loh, Infection and immunity 2021 (secret) - Alteration of the Helicobacter pylori membrane proteome in response to changes in environmental salt concentration
Voss, Proteomics. Clinical applications 2015 - “...2.18 Cytochrome c553 HP1227 HPB8_625 D7FDC5 cellular aromatic compound metabolic process 2.15 4-oxalocrotonate tautomerase (DmpI) HP0924 HPB8_829 * D7FDX9 NA 2.1 Modulator of drug activity B (MDA66) HP0630 HPB8_958 * & D7FEA8 NA 2.07 Flagellar protein FlaG HP0751 HPB8_844 * D7FDZ4 oxidation-reduction process 2.05 NAD(P)H-flavin oxidoreductase...”
- Identification of Helicobacter pylori genes that contribute to stomach colonization
Baldwin, Infection and immunity 2007 - “...into the urease enzyme, respectively. Interestingly, both amiE (HP0924) and amiF (HP1238), two amidases carried in the H. pylori genome, were identified as...”
- Characterization of the ArsRS regulon of Helicobacter pylori, involved in acid adaptation
Pflock, Journal of bacteriology 2006 - “...JHP0228 0.28 HP1022 JHP0402 0.30 HP0890 JHP0823 0.47 HP0924 JHP0858 0.44 HP0954 HP1104 JHP0888 JHP1030 0.45 0.34 JHP0585* 0.27 JHP1429 0.29 HP0891 JHP0824 0.41...”
- Chronic Helicobacter pylori infection with Sydney strain 1 and a newly identified mouse-adapted strain (Sydney strain 2000) in C57BL/6 and BALB/c mice
Thompson, Infection and immunity 2004 - “...HP0102 HP0105 HP0186 HP0720 HP0189 HP0408 HP1353 HP0594 HP0057 HP0924 HP0783 HP0311 HP0823 JHP0950 HP1097 infA thiB omp29 babB cag15 ftsZ tdhF hylB mod hsdR ung...”
jhp0858 putative from Helicobacter pylori J99
36% identity, 81% coverage
For advice on how to use these tools together, see
Interactive tools for functional annotation of bacterial genomes.
The PaperBLAST database links 793,807 different protein sequences to 1,259,118 scientific articles. Searches against EuropePMC were last performed on March 13 2025.
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.
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.
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.
by Morgan Price,
Arkin group
Lawrence Berkeley National Laboratory