PaperBLAST
Full List of Papers Linked to VIMSS10078473
HEMF1 / Q9LR75 coproporphyrinogen III oxidase (EC 1.3.3.3) from Arabidopsis thaliana (see 2 papers)
HEM61_ARATH / Q9LR75 Coproporphyrinogen-III oxidase 1, chloroplastic; AtCPO-I; Coprogen oxidase; Coproporphyrinogenase; Protein LESION INITIATION 2; EC 1.3.3.3 from Arabidopsis thaliana (Mouse-ear cress) (see paper)
Q9LR75 coproporphyrinogen oxidase (EC 1.3.3.3) from Arabidopsis thaliana (see paper)
AT1G03475 LIN2 (LESION INITIATION 2); coproporphyrinogen oxidase from Arabidopsis thaliana
NP_171847 Coproporphyrinogen III oxidase from Arabidopsis thaliana
- function: Key enzyme in heme biosynthesis. Catalyzes the oxidative decarboxylation of propionic acid side chains of rings A and B of coproporphyrinogen III.
catalytic activity: coproporphyrinogen III + O2 + 2 H(+) = protoporphyrinogen IX + 2 CO2 + 2 H2O (RHEA:18257)
subunit: Homodimer.
disruption phenotype: Spontaneous formation of necrotic leaf lesions. - A comprehensive analysis of transcriptomic data for comparison of plants with different photosynthetic pathways in response to drought stress
Karami, PloS one 2023 - “...up-regulated gene protochlorophyllide oxidoreductase A ( PORA ; AT5G54190) and down-regulated genes coproporphyrinogen III oxidase (AT1G03475) and, chlorophyll synthase ( G4 ; AT3G51820), were identified exclusively in C4 plants. The hub gene analysis identified many common top-ranked genes based on the MCC method in both groups...”
- Arabidopsis CIA2 and CIL have distinct and overlapping functions in regulating chloroplast and flower development
Yang, Plant direct 2022 - “...particle 54 kDa subunit (CpSRP54) 0.64 0.95 0.51 0.76 1.21 0.46 CP Chlorophyllbiosynthetic proteins (14) AT1G03475 Coproporphyrinogen III oxidase (CPO1, HEMF1) 0.80 0.97 0.66 0.64 0.94 0.61 CP AT1G44446 Chlorophyllide a oxygenase (CAO, CH1) 0.71 0.97 0.47 0.72 1.04 0.59 CP AT3G48730 Glutamate1semialdehyde aminomutase 2 (GSA2)...”
- BRS1 mediates plant redox regulation and cold responses
Zhang, BMC plant biology 2021 - “...Cytosolic NADP+-dependent isocitrate dehydrogenase Redox 0.22 7* AT1G65930 Cytosolic NADP+-dependent isocitrate dehydrogenase Redox 3.12 8 AT1G03475 Coproporphyrinogen III oxidase Redox 1.15 9 AT5G09530 Proline-rich protein 10 Seed germination 1.24 10 AT1G66200 Cytosolic glutamate synthetase Glutamine biosynthesis 1.79 11 ATCG00490 Ribulose-bisphosphate carboxylase Carbon fixation of photosynthesis 0.79...”
- Review: the effect of light on the key pigment compounds of photosensitive etiolated tea plant
Yue, Botanical studies 2021 - “...6 Uroporphyrinogen III decarboxylase UROD HEME1 At2g40490 HEME2 At3g14930 7 Coproporphyrinogen III oxidase CPOX HEMF1 At1g03475 HEMF2 At4g03205 8 Protoporphyrinogen IX oxidase PPOX HEMG1 At5g14220 HEMG2 At4g01690 9 Magnesium chelatase H subunit CHLH (GUN5) CHLH At5g13630 Magnesium chelatase I subunit CHLI CHLI1 At4g18490 Magnesium chelatase D...”
- Changes in Brassica oleracea Leaves Infected With Xanthomonas campestris pv. campestris by Proteomics Analysis
Tortosa, Frontiers in plant science 2021 - “...4 TRX-M4 M4EEN8 AT3G15360 0.013 1.31 43.8 Auxins signaling 245 Coproporphyrinogen III oxidase CPX1/LIN2 Q9LR75 AT1G03475 0.002 15.62 13 32 Chaperonin 20 CPN20 O65282 AT5G20720 0.016 1.82 79.8 Others 58 Ribosome recycling factor, chloroplast precursor RRF Q9M1 0 AT3G63190 0.003 1.45 54.9 194 Winged-helix DNA-binding transcription...”
- Genetic Mapping of a Light-Dependent Lesion Mimic Mutant Reveals the Function of Coproporphyrinogen III Oxidase Homolog in Soybean
Ma, Frontiers in plant science 2020 - “...( Medtr5g098800 ), Trifolium pretense ( Tp57577 TGAC v2 gene35901 ), and Arabidopsis thaliana ( AT1G03475 ; AT4G03205 ). (B) Synteny diagram plot of the genes surrounding the GmLMM2 gene. (C) Expression pattern of GmLMM2 in different tissues of Williams 82 (WT). (D) GmLMM2 localized to...”
- RANK: Large-Scale Inference with Graphical Nonlinear Knockoffs
Fan, Journal of the American Statistical Association 2020 - “...Starch AT5G19220 Glycol AT4G27600 Starch AT2G21590 Pentos AT3G04790 Trypto AT5G48220 Phenyl AT2G27820 Trypto AT5G17980 Porphy AT1G03475 Mevalo AT5G47720 Porphy AT3G51820...”
- Profiling of advanced glycation end products uncovers abiotic stress-specific target proteins in Arabidopsis
Chaplin, Journal of experimental botany 2019 - “...AT4G14040 4 GLYCERALDEHYDE 3-PHOSPHATE DEHYDROGENASE A SUBUNIT 2 Q9LPW0 AT1G12900 4 LESION INITIATION 2 Q9LR75 AT1G03475 8 GLYCERALDEHYDE-3-PHOSPHATE DEHYDROGENASE C SUBUNIT P25858 AT3G04120 2 PSA E1 KNOCKOUT Q9S831 AT4G28750 2 - 4 GLUTATHIONE S-TRANSFERASE PHI 9 O80852 AT2G30860 5 - 9 RUBISCO SMALL SUBUNIT 3B/RUBISCO SMALL...”
- Co-infection of Sweet Orange with Severe and Mild Strains of Citrus tristeza virus Is Overwhelmingly Dominated by the Severe Strain on Both the Transcriptional and Biological Levels
Fu, Frontiers in plant science 2017 - “...1.19 HEMC Orange1.1g020472m AT5G08280 Hydroxymethylbilane synthase 1.38 HEME2 Orange1.1g016596m AT2G40490 Uroporphyrinogen decarboxylase 1.06 HEMF1 Orange1.1g016102m AT1G03475 Lesion initiation 2 1.03 ATM3 Orange1.1g030870m AT2G15570 Thioredoxin M-Type 3, Chloroplast (Trx-M3) 1.51 ATM3 Orange1.1g030784m AT2G15570 Thioredoxin M-Type 3, Chloroplast (Trx-M3) 1.58 ACHT5 Orange1.1g023089m AT5G61440 Atypical Cys His Rich Thioredoxin...”
- Biotrophy at Its Best: Novel Findings and Unsolved Mysteries of the Arabidopsis-Powdery Mildew Pathosystem
Kuhn, The arabidopsis book 2016 - “...as EDR1 to 4, LESION INITIATION 2 (LIN2: At1g03475), and GSL5/PMR4 are associated with the repression of SA-mediated defense. This is indicated by requirement...”
- Proteomic Insight into the Response of Arabidopsis Chloroplasts to Darkness
Wang, PloS one 2016 - “...Q9C9I7 AT1G71500 T 1.370.03 Chlorophyll and carotenoid synthesis (4) 16 Coproporphyrinogen-III oxidase 1 (CPOX) Q9LR75 AT1G03475 S 1.450.08 17 Magnesium-protoporphyrin IX monomethyl ester [oxidative] cyclase (CRD1) Q9M591 AT3G56940 Ts 1.400.10 18 Protochlorophyllide reductase like protein (POR C) Q0WVW0 AT1G03630 Ts 1.530.09 19 Lycopene beta/epsilon cyclase protein...”
- Differential root transcriptomics in a polyploid non-model crop: the importance of respiration during osmotic stress
Zorrilla-Fontanesi, Scientific reports 2016 (no snippet) - Expression profiling and functional analysis reveals that TOR is a key player in regulating photosynthesis and phytohormone signaling pathways in Arabidopsis
Dong, Frontiers in plant science 2015 - “...1.32 0.86 AT3G56940 Copper response deffect 1(CRD1) 1.11 0.85 AT3G51820 Chlorophyll synthase (CHLG) 1.44 0.86 AT1G03475 Oproporphyrinogen III oxidase (HEMF1) 1.31 0.86 AT5G13630 Genomes uncoupled (GUN5) 1.28 0.86 AT4G25080 Magnesium-protoporphyrin IX methyltransferase (CHLM) 1.15 0.85 AT5G26030 Ferrochelatase I (FC1) 1.12 0.83 Figure 4 AZD induced photosynthesis-related...”
- To die or not to die? Lessons from lesion mimic mutants
Bruggeman, Frontiers in plant science 2015 - “...leaves of juveniles plants Unknown Yamaguchi et al., 2012 ; Yang et al., 2012 lin2 At1g03475 Coproporphyrinogen III oxidase involved in chlorophyll biosynthesis Spontaneous lesions formation on young leaves Probable accumulation of photosensitizing tetrapyrrole intermediates Ishikawa et al., 2001 ; Sun et al., 2011 ; Guo...”
- Proteome and metabolome profiling of cytokinin action in Arabidopsis identifying both distinct and similar responses to cytokinin down- and up-regulation
Černý, Journal of experimental botany 2013 - “...are novel CK-response proteins: three ribosomal proteins, a key enzyme in haem biosynthesis (coproporphyrinogen oxidase, At1g03475), a peroxidase (At3g49120) reportedly involved in cell elongation (Passardi et al. , 2005), and a sterol carrier protein (At5g42890) with a loss-of-function mutation phenotype correlating with known CK effects on...”
- “...and metabolites indicative of endogenous cytokinin levels ID (AGI/KEGG) Recommended name Correlation with cytokinin levels At1g03475 Coproporphyrinogen-III oxidase, chloroplastic Positive At1g05190 50S ribosomal protein L6, chloroplastic Positive At1g79040 Photosystem II 10kDa polypeptide, chloroplastic Positive At2g36460 Fructose-bisphosphate aldolase Positive At3g07110 60S ribosomal protein L13a-1 Positive At3g09200 60S...”
- Physical Mapping in a Triplicated Genome: Mapping the Downy Mildew Resistance Locus Pp523 in Brassica oleracea L
Carlier, G3 (Bethesda, Md.) 2011 - “...51P12 At1g06930 NS Map F C8a 159P2 Not Seq Not Seq PCR C5 111P15 NS At1g03475 PCR C8a 76C8 At1g07510 At1g07200 PCR C8a 62B20 NS At1g07230 Map R C5 13N3 NS At1g03890 Map R C8a 18P4 NS At1g07200 PCR C8a 52A2 At1g07570 At1g07260 PCR C5 40J10...”
- Proteomic analysis of extracellular ATP-regulated proteins identifies ATP synthase beta-subunit as a novel plant cell death regulator
Chivasa, Molecular & cellular proteomics : MCP 2011 - “...At1g77120 At5g08690 At3g29360 At1g62380 At3g14990 At1g03475 At5g08670 At2g44060 At3g18130 At4g34050 Atmg01190 At4g13940 At4g13940 At2g21250 At5g15650 At3g56090...”
- Tetrapyrrole Metabolism in Arabidopsis thaliana
Tanaka, The arabidopsis book 2011 - “...al. 1995a), maize (Williams et al. 2006) and Arabidopsis (At1g03475) (Ishikawa et al. 2001). Antisense hemF lines of tobacco (Kruse et al. 1995b) and a hemF...”
- Differential proteomic analysis of Arabidopsis thaliana genotypes exhibiting resistance or susceptibility to the insect herbivore, Plutella xylostella
Collins, PloS one 2010 - “...61 3 33.6/6.0 39.2/7.0 SW vs. RW= a SW vs. RW=0.048 10 Coprogen oxidase, putative At1g03475 PAYIPIVEKIESILVSLPLSAR 65 c 7 36.5/6.1 34.2/5.6 RD vs. RW= a , SD vs. SW= a RD vs. RW=0.036, SD vs. SW=0.000 11 Glutamate-1-semialdehyde aminotransferase At3g48730 AGSGVATLGLPDSPGVPKLSQPGTYEYLDK 79 6 47.7/6.4 50.1/7.0...”
- Computational prediction of miRNAs in Arabidopsis thaliana
Adai, Genome research 2005 - “...were found for two other SRPFs (At4g03205 and At1g03475), as well as transcripts encoding an (MIR164 and MIR170/171). The largest number of newly...”
- “...uaaUACCCGAACCCGAACCGAUacc Predicted miRNA sequencec At4g03205 At1g03475 At5g07280 At1g60720 At1g56130 At1g61520 At1g27340JR At1g10200 At4g24850/60* At5g20580...”
- A mutation in a coproporphyrinogen III oxidase gene confers growth inhibition, enhanced powdery mildew resistance and powdery mildew-induced cell death in Arabidopsis.
Guo, Plant cell reports 2013 (PubMed)- GeneRIF: LIN2 negatively regulates resistance to powdery mildew and oomycete pathogens.
- Proteomic Analysis of Proteins Related to Defense Responses in Arabidopsis Plants Transformed with the rolB Oncogene
Vereshchagina, International journal of molecular sciences 2023 - “...and drought 1.5 Photosynthesis 1 Q9SW18 Magnesium protoporphyrin IX methyltransferase, chloroplastic Chlorophyll biosynthesis 3.0 2 Q9LR75 Coproporphyrinogen-III oxidase 1, chloroplastic Chlorophyll biosynthesis 5.0 3 O22886 Uroporphyrinogen decarboxylase 2, chloroplastic Chlorophyll biosynthesis 2.8 4 P21218 Protochlorophyllide reductase B, chloroplastic Chlorophyll biosynthesis 2.4 5 O48741 Protochlorophyllide reductase C,...”
- New In Vivo Approach to Broaden the Thioredoxin Family Interactome in Chloroplasts
Ancín, Antioxidants (Basel, Switzerland) 2022 - “...Soluble inorganic pyrophosphatase 6 (Ppase 6) 74.6 0 stroma Chlorophyll synthesis A0A1S4C5X4 Oxygen-dependent coproporphyrinogen-III oxidase Q9LR75 Coproporphyrinogen-III oxidase 1 (CPOX) 80.4 2 stroma Photorespiration A0A1S3X073 Phosphoglycolate phosphatase 1B P0DKC4 Phosphoglycolate phosphatase 1B 66.8 4 stroma PSII assembly A0A1S4DN09 Photosystem II repair protein PSB27-H1 Q9LR64 Photosystem II...”
- Commonalities and specialties in photosynthetic functions of PROTON GRADIENT REGULATION5 variants in Arabidopsis
Penzler, Plant physiology 2022 - “...Q9FJ81 CCB2 Cofactor Assembly of Complex C subunit B 0.668 6.62 E 03 Chlorophyll biosynthesis Q9LR75; Q93Z96 HEMF1; 2 Coproporphyrinogen-III oxidase 1; 2 1.504 2.04 E 02 Q9FNB0 CHLH Magnesium-chelatase subunit ChlH 1.600 1.85 E 02 P16127 CHLI Magnesium-chelatase subunit ChlI-1 1.885 7.40 E 03 Q43316...”
- Changes in Brassica oleracea Leaves Infected With Xanthomonas campestris pv. campestris by Proteomics Analysis
Tortosa, Frontiers in plant science 2021 - “...M-type 4 TRX-M4 M4EEN8 AT3G15360 0.013 1.31 43.8 Auxins signaling 245 Coproporphyrinogen III oxidase CPX1/LIN2 Q9LR75 AT1G03475 0.002 15.62 13 32 Chaperonin 20 CPN20 O65282 AT5G20720 0.016 1.82 79.8 Others 58 Ribosome recycling factor, chloroplast precursor RRF Q9M1 0 AT3G63190 0.003 1.45 54.9 194 Winged-helix DNA-binding...”
- Sexual and Apogamous Species of Woodferns Show Different Protein and Phytohormone Profiles
Fernández, Frontiers in plant science 2021 - “...237628-108_3_ORF2 (+2) 50 P16127 0 1.58 14 7 Coproporphyrinogen-III oxidase 1 639 263607-90_6_ORF2 (+1) 46 Q9LR75 0 3.00 11 3 Carbamoyl-phosphate synthase large chain 1,088 39629-404_3_ORF2 [3] 133 Q42601 0 1.32 2.6 3 Argininosuccinate synthase 740 1466-1535_4_ORF1 [4] 52 Q9SZX3 0 1.00 7.1 3 Prohibitin-3 372...”
- Profiling of advanced glycation end products uncovers abiotic stress-specific target proteins in Arabidopsis
Chaplin, Journal of experimental botany 2019 - “...Q93WN0 AT4G14040 4 GLYCERALDEHYDE 3-PHOSPHATE DEHYDROGENASE A SUBUNIT 2 Q9LPW0 AT1G12900 4 LESION INITIATION 2 Q9LR75 AT1G03475 8 GLYCERALDEHYDE-3-PHOSPHATE DEHYDROGENASE C SUBUNIT P25858 AT3G04120 2 PSA E1 KNOCKOUT Q9S831 AT4G28750 2 - 4 GLUTATHIONE S-TRANSFERASE PHI 9 O80852 AT2G30860 5 - 9 RUBISCO SMALL SUBUNIT 3B/RUBISCO...”
- Proteomic Insight into the Response of Arabidopsis Chloroplasts to Darkness
Wang, PloS one 2016 - “...(PSB33) Q9C9I7 AT1G71500 T 1.370.03 Chlorophyll and carotenoid synthesis (4) 16 Coproporphyrinogen-III oxidase 1 (CPOX) Q9LR75 AT1G03475 S 1.450.08 17 Magnesium-protoporphyrin IX monomethyl ester [oxidative] cyclase (CRD1) Q9M591 AT3G56940 Ts 1.400.10 18 Protochlorophyllide reductase like protein (POR C) Q0WVW0 AT1G03630 Ts 1.530.09 19 Lycopene beta/epsilon cyclase...”
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