PaperBLAST
PaperBLAST Hits for Pf1N1B4_1829 (83 a.a., MNNVAIAAID...)
Show query sequence
>Pf1N1B4_1829
MNNVAIAAIDLGKHTFHLHAQDDRGHEVYRKKFTRTALTRHLANLAPCTVVMEACGGAHF
MAQEVAKLGHTPKLIALISCVRM
Running BLASTp...
Found 18 similar proteins in the literature:
SA100 IS110-like element IS5075 family transposase from Escherichia coli
KPHS_p200210 transposase InsD1 for insertion sequence IS4321R from Klebsiella pneumoniae subsp. pneumoniae HS11286
58% identity, 23% coverage
- Phage-Derived Endolysins Against Resistant Staphylococcus spp.: A Review of Features, Antibacterial Activities, and Recent Applications
Golban, Infectious diseases and therapy 2025 - “...in the peptidoglycan of S. aureus [ 65 ]. The structural variance between XZ.700 and SA100 endolysins stems from removing a 44-amino-acid linker region at the N-terminus of the Ply2638 amidase domain in XZ.700. This modification in XZ.700 enhanced its antibacterial activity, showing how optimization of...”
- Occurrence of cfr-Positive Linezolid-Susceptible Staphylococcus aureus and Non-aureus Staphylococcal Isolates from Pig Farms
Lee, Antibiotics (Basel, Switzerland) 2023 - “...were generated and then electroporated into the two linezolid-susceptible strains of RN4220 and ST398 MRSA SA100, which were negative for both cfr and fexA genes. As expected, the cfr -positive SA12 strain showed resistant phenotype to linezolid (MIC of 16 mg/L) and all the other four...”
- “...( Table 3 ). Complementation of the linezolid-susceptible S. aureus strains, RN4220 and ST398 MRSA SA100, with plasmids expressing the wild-type cfr resulted in 4-fold increase in linezolid MICs compared to those of the control strains carrying empty pRB474 plasmid ( Table 3 ). In addition...”
- Natural compounds as safe therapeutic options for ulcerative colitis
Gupta, Inflammopharmacology 2022 - “...in patients suffering from UC The study evaluates the safety and preliminary efficacy of oral SA100 in the treatment of patients with mild, moderate or severe UC https://www.clinicaltrials.gov/ct2/show/record/NCT02442960 NCT00374725 Treatment of ulcerative colitis with a combination of Lactobacillus rhamnosus and Lactobacillus acidophilus February 2003/not provided Aarhus...”
- Linker-Improved Chimeric Endolysin Selectively Kills Staphylococcus aureus In Vitro, on Reconstituted Human Epidermis, and in a Murine Model of Skin Infection
Eichenseher, Antimicrobial agents and chemotherapy 2022 - “...construct encoding an N-terminally His-tagged version of a fusion protein subsequently named Staphefekt SA.100 (pHM23LST_Ami2638_SH3b2638; SA100) was then obtained by inserting a fragment corresponding to the M23 domain of lysostaphin into the BamHI/SacI site of pHAmi2638_SH3b2638. This construct was initially generated to allow for direct comparison...”
- Irritable Bowel Syndrome Therapeutic Has Broad-Spectrum Antimicrobial Activity
Cunningham, Antimicrobial agents and chemotherapy 2021 (secret) - Pathogenicity Factors of Genomic Islands in Intestinal and Extraintestinal <i>Escherichia coli</i>
Desvaux, Frontiers in microbiology 2020 - “...). Nonetheless, SHI-3 remains very closely related to the 30-kb SHI-2 in S. flexneri 2a SA100 ( Vokes et al., 1999 ) and 23.8-kb SHI-2 in S. flexneri 5a M90T ( Moss et al., 1999 ), and it belongs to the same family of PAI. The...”
- Complete genome sequence and annotation of the laboratory reference strain Shigella flexneri serotype 5a M90T and genome-wide transcriptional start site determination
Cervantes-Rivera, BMC genomics 2020 - “...were reported in other S. flexneri strains. For example, a screen of S. flexneri 2a SA100 chromosomal fragments fused to promoterless gfp revealed a wealth of metabolic genes that are overexpressed intracellularly [ 36 ], which were characterized in depth in several follow up studies. A...”
- Identification and Characterization of Conjugative Plasmids That Encode Ciprofloxacin Resistance in Salmonella
Chen, Antimicrobial agents and chemotherapy 2018 - “...ampicillin; MRP, meropenem; SXT, trimethoprim-sulfamethoxazole. aID, TC-Sa81 Sa100 TC-Sa100 Sa76 TC-Sa76 Sa117 TC-Sa117 Sa4 TC-Sa4 Sa48 Strain ID ATCC 25922 J53...”
- “...PacBio sequencing platforms. Strains Sa63, Sa81, and Sa100 were found to harbor IncFIB(K) plasmids, namely, pSa63-CIP (GenBank accession number MG874043),...”
- More
- Use of a combined antibacterial synergy approach and the ANNOgesic tool to identify novel targets within the gene networks of multidrug-resistant Klebsiella pneumoniae
Lee, mSystems 2024 - “...RNA_thermometer_1593 NC_016845.1 + KPHS_31510 3134900 3134984 RF01859 Phe_leader 4.9E05 23.4 1 85 RNA_thermometer_19 NC_016846.1 - KPHS_p200210 7230 7296 RF01804 Lambda_thermo 0.00067 14.5 1 67 a Three different RNA thermometers with eight associated genes were identified in the K56_Co Che condition. According to the initial ANNOgesic prediction,...”
Q93EZ2 IS1328 transposase from Shigella flexneri 2a
55% identity, 23% coverage
BCAM0771 putative transposase from Burkholderia cenocepacia J2315
55% identity, 22% coverage
PSPTO_2167 ISPsy7, transposase from Pseudomonas syringae pv. tomato str. DC3000
48% identity, 22% coverage
VPA1254 putative IS1328 transposase from Vibrio parahaemolyticus RIMD 2210633
43% identity, 22% coverage
- Gamma-Mobile-Trio systems define a new class of mobile elements rich in bacterial defensive and offensive tools
Mahata, 2023 - Genomic Features of Environmental and Clinical Vibrio parahaemolyticus Isolates Lacking Recognized Virulence Factors Are Dissimilar
Ronholm, Applied and environmental microbiology 2016 - “...VP0400, VP0402, VP0403 ISF-29-3 VP0387 to VP0395 HS-22-14 VPA1254, VPA1256, VPA1258 to VPA1259, VPA1262 to VPA1265, VPA1267 VPAI-5 (VP2900 to VP2910) VPAI-4...”
- Comparative genomic analysis using microarray demonstrates a strong correlation between the presence of the 80-kilobase pathogenicity island and pathogenicity in Kanagawa phenomenon-positive Vibrio parahaemolyticus strains
Izutsu, Infection and immunity 2008 - “...VPA0448 44.2 VPC-10 25 VPA0889 VPA0913 48.2 VPC-11 17 VPA1254 VPA1270 43.4 VPC-12 VPC-13 87 10 VPA1310 VPA1700 VPA1396 VPA1709 39.2 49.1 a b c Start site...”
- Four genomic islands that mark post-1995 pandemic Vibrio parahaemolyticus isolates
Hurley, BMC genomics 2006 - “...presence of 3 additional regions, VPaI-4 (VP2131 to VP2144), VPaI-5 (VP2900 to VP2910) and VPaI-6 (VPA1254 to VPA1270) by PCR assays and Southern blot analyses among the same set of V. parahaemolyticus isolates. These 3 VPaI regions also gave similar distribution patterns amongst the 41 strains...”
- “...of novel DNA at this site (Figure 3A ). The 27 kb VPaI-6 region encompassed VPA1254 to VPA1270 and encoded an integrase, 3, 4 dihydroxy-2-butanone-4 phos (DHBP) synthase, two putative colicin proteins, a hydrolase and a number of hypothetical proteins. The homologous core chromosomal flanking genes...”
HW44_RS16715 IS110 family transposase from Nitrosococcus oceani
38% identity, 51% coverage
- High Synteny and Sequence Identity between Genomes of Nitrosococcus oceani Strains Isolated from Different Oceanic Gyres Reveals Genome Economization and Autochthonous Clonal Evolution
Wang, Microorganisms 2020 - “...genes predicted to encode transposase in the IS1 family (HW44_RS17215, HW44_RS17265, and HW44_RS17705), IS110 family (HW44_RS16715, HW44_RS16590, HW44_RS18070, and HW44_RS18130), ISAzo13 family (HW44_RS15500, HW44_RS15595, and HW44_RS18005) and ISNCY family (HW44_RS15525 and RS1562) are uniquely present in the genome of AFC132 but not the other N. oceani...”
PA3434 probable transposase from Pseudomonas aeruginosa PAO1
PA0445 probable transposase from Pseudomonas aeruginosa PAO1
PA2319 probable transposase from Pseudomonas aeruginosa PAO1
PA2690 probable transposase from Pseudomonas aeruginosa PAO1
PA3993 probable transposase from Pseudomonas aeruginosa PAO1
PA4797 probable transposase from Pseudomonas aeruginosa PAO1
42% identity, 22% coverage
- Loss of RNA Chaperone Hfq Unveils a Toxic Pathway in Pseudomonas aeruginosa
Hill, Journal of bacteriology 2019 (secret) - The IS1111 family members IS4321 and IS5075 have subterminal inverted repeats and target the terminal inverted repeats of Tn21 family transposons
Partridge, Journal of bacteriology 2003 - “...no. AE004481-2, PA2319 in AE004658, PA2690 in AE004697, PA3434 in AE004764, PA3993 in AE004817, and PA4797 in AE004892-3) that is 42.6% identical to that...”
- Genotypic and phenotypic variation in Pseudomonas aeruginosa reveals signatures of secondary infection and mutator activity in certain cystic fibrosis patients with chronic lung infections
Warren, Infection and immunity 2011 - “...Boundary I series Size (bp) I1 6,568 PA0442 PA0445 PA0642 PA0715-PA0717 PA0724 PA0820 PA0977 PA0980-PA0981 PA0983-PA0985 PA0992-PA0993 116 1,016 788 3,387 1,262...”
- Transcriptome analysis reveals that multidrug efflux genes are upregulated to protect Pseudomonas aeruginosa from pentachlorophenol stress
Muller, Applied and environmental microbiology 2007 - “...University of California, Berkeley PA0355 (pfpI) PA0417 (chpE) PA0445 PA0526 PA0633 PA0726 PA0868 (RF-1) PA1281 (cobV) PA1393 (cysC) PA1705 (pcrG) PA1780 (nirD)...”
- The IS1111 family members IS4321 and IS5075 have subterminal inverted repeats and target the terminal inverted repeats of Tn21 family transposons
Partridge, Journal of bacteriology 2003 - “...a gene encoding a transposase (open reading frames PA0445 in GenBank accession no. AE004481-2, PA2319 in AE004658, PA2690 in AE004697, PA3434 in AE004764,...”
- The IS1111 family members IS4321 and IS5075 have subterminal inverted repeats and target the terminal inverted repeats of Tn21 family transposons
Partridge, Journal of bacteriology 2003 - “...reading frames PA0445 in GenBank accession no. AE004481-2, PA2319 in AE004658, PA2690 in AE004697, PA3434 in AE004764, PA3993 in AE004817, and PA4797 in...”
- Pseudomonas aeruginosa Genome Evolution in Patients and under the Hospital Environment
Lucchetti-Miganeh, Pathogens (Basel, Switzerland) 2014 - “...probably highlighting a defect in mucoidy conversion in ST395 strains. Another example comes from the PA2690 gene in PAO1 which encodes a probable transposase which is absent from the ST395 strain genomes. Interestingly, ST395 strains possess as B136-33, 2192 and RP73 and PSE9 [ 61 ]...”
- The IS1111 family members IS4321 and IS5075 have subterminal inverted repeats and target the terminal inverted repeats of Tn21 family transposons
Partridge, Journal of bacteriology 2003 - “...in GenBank accession no. AE004481-2, PA2319 in AE004658, PA2690 in AE004697, PA3434 in AE004764, PA3993 in AE004817, and PA4797 in AE004892-3) that is 42.6%...”
- Global identification of RsmA/N binding sites in Pseudomonas aeruginosa by in vivo UV CLIP-seq
Chihara, RNA biology 2021 (secret) - The IS1111 family members IS4321 and IS5075 have subterminal inverted repeats and target the terminal inverted repeats of Tn21 family transposons
Partridge, Journal of bacteriology 2003 - “...PA2319 in AE004658, PA2690 in AE004697, PA3434 in AE004764, PA3993 in AE004817, and PA4797 in AE004892-3) that is 42.6% identical to that of IS4321, but the...”
- Whole genome and transcriptome analyses of environmental antibiotic sensitive and multi-resistant Pseudomonas aeruginosa isolates exposed to waste water and tap water
Schwartz, Microbial biotechnology 2015 - “...n.p. 57 45 gi|410609201 Transposase n.p. n.p. 2789 2351 gi|446985433 Integrase n.p. n.p. 0 1 PA4797 Probable transposase n.p. n.p. 1294 879 gi|496684684 Conjugal transfer protein TrbE n.p. n.p. 28 27 gi|496684684 Conjugal transfer protein TrbE n.p. n.p. 13 15 gi|496684684 Conjugal transfer protein TrbE n.p....”
- Fitness of isogenic colony morphology variants of Pseudomonas aeruginosa in murine airway infection
Rakhimova, PloS one 2008 - “...- Probable iron-sulfur protein PA4703 - - Hypothetical protein; predicted regulator of competence-specific genes (TfoX) PA4797 - - Probable transposase. PA4949 - - Conserved hypothetical protein; predicted sugar kinase PA4951 - orn Transcription, RNA processing and degradation, oligoribonuclease PA5121 - - Hypothetical membrane protein; predicted small-conductance...”
- The IS1111 family members IS4321 and IS5075 have subterminal inverted repeats and target the terminal inverted repeats of Tn21 family transposons
Partridge, Journal of bacteriology 2003 - “...in AE004697, PA3434 in AE004764, PA3993 in AE004817, and PA4797 in AE004892-3) that is 42.6% identical to that of IS4321, but the boundaries of the IS have...”
HJ586_02470 IS110-like element ISEch3 family transposase from Dickeya zeae
42% identity, 22% coverage
Q7WWT0 IS110-like element IS884 family transposase from Cupriavidus necator (strain ATCC 17699 / DSM 428 / KCTC 22496 / NCIMB 10442 / H16 / Stanier 337)
40% identity, 22% coverage
PSPPH_A0132 ISPsy16, transposase from Pseudomonas syringae pv. phaseolicola 1448A
42% identity, 23% coverage
YE1870 putative transposase for IS1667 from Yersinia enterocolitica subsp. enterocolitica 8081
40% identity, 21% coverage
YE105_C3382 IS110-like element ISYen1 family transposase from Yersinia enterocolitica subsp. palearctica 105.5R(r)
40% identity, 22% coverage
YE3064 putative transposase for IS1667 from Yersinia enterocolitica subsp. enterocolitica 8081
YE1359 putative transposase for IS1667 from Yersinia enterocolitica subsp. enterocolitica 8081
40% identity, 22% coverage
CCNA_02826 transposase from Caulobacter crescentus NA1000
37% identity, 20% coverage
CC2740 IS1111A/IS1328/IS1533 family transposase from Caulobacter crescentus CB15
37% identity, 19% coverage
XNC1_3131 IS110 family transposase from Xenorhabdus nematophila ATCC 19061
34% identity, 20% coverage
CBU_1090 IS1111A transposase from Coxiella burnetii RSA 493
CBU_0040 IS1111A transposase from Coxiella burnetii RSA 493
CBU_1186 IS1111A transposase from Coxiella burnetii RSA 493
CBU_1217a transposase from Coxiella burnetii RSA 493
32% identity, 21% coverage
- Ultrasensitive Detection of Pathogenic Bacteria by Targeting High Copy Signature Genes
Dong, Frontiers in veterinary science 2022 - “...strain Gene locus Copy number Function description Coxiella burnetii RSA 493 CBU_1076 20 IS1111A transposase CBU_1090 20 IS1111A transposase CBU_1186 20 IS1111A transposase CBU_1269a 18 hypothetical protein CBU_1758b 16 hypothetical protein CBU_1716b 6 hypothetical protein CBU_1061a 5 hypothetical protein CBU_1555 3 ISAs1 family transposase Mycobacterium tuberculosis...”
- Horizontally Acquired Biosynthesis Genes Boost Coxiella burnetii's Physiology
Moses, Frontiers in cellular and infection microbiology 2017 - “...S1 ), indicating that the genes were transferred en bloc. In addition, an IS1111A transposase (CBU_0040) is proximally located to the operon, illustrating a probable role for this mobile genetic element in HGT (Figure 3B ). Based on homology, CBU_0034 to CBU_0038 encode ACP, FabB, FabZ,...”
- Ultrasensitive Detection of Pathogenic Bacteria by Targeting High Copy Signature Genes
Dong, Frontiers in veterinary science 2022 - “...number Function description Coxiella burnetii RSA 493 CBU_1076 20 IS1111A transposase CBU_1090 20 IS1111A transposase CBU_1186 20 IS1111A transposase CBU_1269a 18 hypothetical protein CBU_1758b 16 hypothetical protein CBU_1716b 6 hypothetical protein CBU_1061a 5 hypothetical protein CBU_1555 3 ISAs1 family transposase Mycobacterium tuberculosis H37Rv Rv1756c 16 Transposase...”
- Identification of novel MITEs (miniature inverted-repeat transposable elements) in Coxiella burnetii: implications for protein and small RNA evolution
Wachter, BMC genomics 2018 - “...certain IS1111 TEs. For example, it is likely that the IS1111 transposons at CBU_1217a and CBU_1186 in the RSA 493 strain inserted into these positions after divergence from the Dugway strain, because in Dugway there are full-size QMITE2 copies with discernible DRs that have no IS1111...”
- Identification of novel MITEs (miniature inverted-repeat transposable elements) in Coxiella burnetii: implications for protein and small RNA evolution
Wachter, BMC genomics 2018 - “...transposition of certain IS1111 TEs. For example, it is likely that the IS1111 transposons at CBU_1217a and CBU_1186 in the RSA 493 strain inserted into these positions after divergence from the Dugway strain, because in Dugway there are full-size QMITE2 copies with discernible DRs that have...”
CBU_1076 IS1111A transposase from Coxiella burnetii RSA 493
32% identity, 21% coverage
- Ultrasensitive Detection of Pathogenic Bacteria by Targeting High Copy Signature Genes
Dong, Frontiers in veterinary science 2022 - “...bovis . Species and strain Gene locus Copy number Function description Coxiella burnetii RSA 493 CBU_1076 20 IS1111A transposase CBU_1090 20 IS1111A transposase CBU_1186 20 IS1111A transposase CBU_1269a 18 hypothetical protein CBU_1758b 16 hypothetical protein CBU_1716b 6 hypothetical protein CBU_1061a 5 hypothetical protein CBU_1555 3 ISAs1...”
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