PaperBLAST
PaperBLAST Hits for sp|Q9HY60|ARNE_PSEAE Probable 4-amino-4-deoxy-L-arabinose-phosphoundecaprenol flippase subunit ArnE OS=Pseudomonas aeruginosa (strain ATCC 15692 / DSM 22644 / CIP 104116 / JCM 14847 / LMG 12228 / 1C / PRS 101 / PAO1) OX=208964 GN=arnE PE=3 SV=1 (115 a.a., MSAALLLATL...)
Show query sequence
>sp|Q9HY60|ARNE_PSEAE Probable 4-amino-4-deoxy-L-arabinose-phosphoundecaprenol flippase subunit ArnE OS=Pseudomonas aeruginosa (strain ATCC 15692 / DSM 22644 / CIP 104116 / JCM 14847 / LMG 12228 / 1C / PRS 101 / PAO1) OX=208964 GN=arnE PE=3 SV=1
MSAALLLATLLMTGLGQVAQKLTVEHWRLVAADGWTARLRSPWPWLALLALGLGLLCWLL
LLQRVEVGSAYPMLALNFVLVTLAARFVFDEPVDRRHLAGLLLIVAGVALLGRSA
Running BLASTp...
Found 15 similar proteins in the literature:
PA3557 hypothetical protein from Pseudomonas aeruginosa PAO1
100% identity, 100% coverage
- Human host defense peptide LL-37 stimulates virulence factor production and adaptive resistance in Pseudomonas aeruginosa
Strempel, PloS one 2013 - “...arnC ArnC +1.6 PA3555 arnD ArnD +1.5 PA3556 arnT Inner membrane L-Ara4N transferase ArnT +2.0 PA3557 arnE ArnE +2.0 PA3558 arnF ArnF +2.2 PA3559 ugd Probable nucleotide sugar dehydrogenase +2.8 Two-component system PmrA-PmrB PA4773 Hypothetical protein +4.9 PA4774 Hypothetical protein +3.2 PA4775 Hypothetical protein +2.2 PA4776...”
- The two-component system CprRS senses cationic peptides and triggers adaptive resistance in Pseudomonas aeruginosa independently of ParRS
Fernández, Antimicrobial agents and chemotherapy 2012 - “...PA3554 PA3555 PA3556 8 8 0.5 0.5 0.5 0.5 1-2 2-4 8 8 PA3557 PA3558 PA3559 In minimal medium with low (20 M) Mg2 Polymyxin B Colistin 16 32 8 32 8 16 8 32 8 32 a...”
- A two-component regulatory system interconnects resistance to polymyxins, aminoglycosides, fluoroquinolones, and β-lactams in Pseudomonas aeruginosa
Muller, Antimicrobial agents and chemotherapy 2011 - “...28.9 14.3 45.7 4.6 25.5 33.6 11.0 11.6 15.3 8.5 PA3557 PA3558 PA3559 arnE (pmrL) arnF (pmrM) ugd (pmrE) 3.1 9.2 16.1 PA4773 PA4774 PA4775 oprD mexY 36.8 12.5...”
- The sensor kinase CbrA is a global regulator that modulates metabolism, virulence, and antibiotic resistance in Pseudomonas aeruginosa
Yeung, Journal of bacteriology 2011 - “...PA1178 PA1170 PA1797 PA2198 PA3552 PA3553 PA3554 PA3555 PA3556 PA3557 PA3558 pvdA pvdE pvdD algG htpG htpX ibpA arnB arnC arnA arnD arnT arnE arnF a ID,...”
- Polyamines induce resistance to cationic peptide, aminoglycoside, and quinolone antibiotics in Pseudomonas aeruginosa PAO1
Kwon, Antimicrobial agents and chemotherapy 2006 - “...PA1178 PA1179 PA1180 PA3552 PA3553 PA3554 PA3555 PA3556 PA3557 PA3558 PA3559 PA4776 PA4777 Gene expression (relative ratio) inb: 1618 KWON AND LU ANTIMICROB....”
- Contribution of the PhoP-PhoQ and PmrA-PmrB two-component regulatory systems to Mg2+-induced gene regulation in Pseudomonas aeruginosa
McPhee, Journal of bacteriology 2006 - “...PA0762b PA0763b PA0764b PA1297 PA3552 PA3553 PA3554 PA3555 PA3556 PA3557 PA3558 PA3559 PA3920 P value H851 with low Mg2 concn vs H103 with high Mg2 concn Mg2...”
PA14_18320 putative inner membrane protein from Pseudomonas aeruginosa UCBPP-PA14
99% identity, 100% coverage
HZ99_RS09315 4-amino-4-deoxy-L-arabinose-phosphoundecaprenol flippase subunit ArnE from Pseudomonas paracarnis
65% identity, 85% coverage
- Combined Transcriptome and Proteome Analysis of RpoS Regulon Reveals Its Role in Spoilage Potential of Pseudomonas fluorescens
Liu, Frontiers in microbiology 2019 - “...WP_038442550.1 4-deoxy-4-formamido-L-arabinose-phosphoundecaprenol deformylase ArnD 0.069 (1.15E-06) Down/ HZ99_RS09310 WP_038442551.1 4-amino-4-deoxy-L-arabinose transferase ArnT 0.069 (5.68E-04) Down/ HZ99_RS09315 WP_038442552.1 4-amino-4-deoxy-L-arabinose-phospho-UDP flippase ArnE 0.175 (4.61E-02) Down/ HZ99_RS09325 WP_038442554.1 UDP-glucose 6-dehydrogenase 0.100 (4.32E-06) 0.442 (3.52E-03) Down/Down HZ99_RS26590 WP_038447400.1 Glycosyl transferase 0.443 (1.87E-02) /Down STRESS RESPONSES HZ99_RS02240 WP_038441046.1 Peroxiredoxin AhpC 0.809...”
ArnE / b4544 undecaprenyl-phosphate-α-L-Ara4N flippase - ArnE subunit from Escherichia coli K-12 substr. MG1655 (see 2 papers)
ArnE / Q47377 undecaprenyl-phosphate-α-L-Ara4N flippase - ArnE subunit from Escherichia coli (strain K12) (see 6 papers)
ARNE_ECOLI / Q47377 Probable 4-amino-4-deoxy-L-arabinose-phosphoundecaprenol flippase subunit ArnE; L-Ara4N-phosphoundecaprenol flippase subunit ArnE; Undecaprenyl phosphate-aminoarabinose flippase subunit ArnE from Escherichia coli (strain K12) (see paper)
TC 2.A.7.22.1 / Q47377 Probable 4-amino-4-deoxy-L-arabinose-phosphoundecaprenol flippase subunit ArnE, component of 4-amino-4-deoxy-L-arabinose phosphoundecaprenol flippase, ArnEF [ArnE, 111aas; 4 TMSs; PmrL; YfbW] [ArnF, 128aas; 4 TMSs; PmrM; YfbJ] Functions in modification of lipid A during biosynthesis of lipopolysaccharide. Required for resistance to polymyxin and cationic antimicrobial peptides from Escherichia coli (strain K12) (see 5 papers)
yfbW / EW|b4544 inner membrane protein yfbW from Escherichia coli K12 (see 7 papers)
b4544 hypothetical protein from Escherichia coli str. K-12 substr. MG1655
56% identity, 50% coverage
- function: Translocates 4-amino-4-deoxy-L-arabinose-phosphoundecaprenol (alpha-L-Ara4N-phosphoundecaprenol) from the cytoplasmic to the periplasmic side of the inner membrane.
subunit: Heterodimer of ArnE and ArnF.
disruption phenotype: Cells lacking this gene lack L-Ara4N-modified lipid A and are sensitive to polymyxin. - substrates: 4-amino-4-deoxy-L-arabinose phosphoundecaprenol, Cationic antimicrobial peptides, Polymyxin
- Genome-Scale Mapping of Escherichia coli σ54 Reveals Widespread, Conserved Intragenic Binding
Bonocora, PLoS genetics 2015 - “...294 10.808 IS28 2370326 2 C TGGC ATGGAGCC TGC A 2370324 + b2257 arnT + b4544 arnE 253 10.155 IS29 2484404 11 C TGGC ATACATTA TGC A 2484401 + b2370 evgS + b2376 ypdI 8316 12.682 IS30 2526524 6 T TGGC ATTGTCG TTGC A 2526536 -...”
- The serum resistome of a globally disseminated multidrug resistant uropathogenic Escherichia coli clone
Phan, PLoS genetics 2013 - “...0.5 R EC958_2594 arnD b2256 undecaprenyl phosphate-alpha-L-ara4FN deformylase 2 WT 0.063 WT G EC958_2596 arnE b4544 ArnE/ArnF undecaprenyl-phosphate--L-Ara4N flippase 1 WT WT WT P EC958_2597 arnF b2258 ArnE/ArnF undecaprenyl-phosphate--L-Ara4N flippase 2 WT WT WT - EC958_2652 dedA b2317 conserved inner membrane protein 1 b WT WT...”
- An undecaprenyl phosphate-aminoarabinose flippase required for polymyxin resistance in Escherichia coli
Yan, The Journal of biological chemistry 2007 - “...b2253 YfbF, Orf2, b2254 YfbH, Orf4, b2256 YfbW, Orf6, b4544 YfbJ, Orf7, b2258 YfbI, Orf5, b2257 This nomenclature was used by Gunn et al. (16) for Salmonella....”
EC958_2596 4-amino-4-deoxy-L-arabinose-phosphoundecaprenol flippase subunit ArnE from Escherichia coli O25b:H4-ST131
56% identity, 50% coverage
KP1_5179 hypothetical protein from Klebsiella pneumoniae NTUH-K2044
VK055_3628 4-amino-4-deoxy-L-arabinose-phosphoundecaprenol flippase subunit ArnE from Klebsiella pneumoniae subsp. pneumoniae
56% identity, 50% coverage
- The Capsule Regulatory Network of Klebsiella pneumoniae Defined by density-TraDISort
Dorman, mBio 2018 - “...l -arabinose-phosphoundecaprenol flippase subunit ArnF 1.00 KP1_5178 VK055_3630 arnE SMR family multidrug resistance protein 0.95 KP1_5179 VK055_3628 arnD Polymyxin resistance protein PmrJ 1.00 KP1_5181 VK055_3626 gor Glutathione reductase 1.00 KP1_5206 VK055_3604 wabN Deacetylase 1.00 KP1_5319 VK055_3502 wecA Undecaprenyl-phosphate N-acetylglucosaminyl 1-phosphate transferase 0.98 KP1_0146 VK055_3191 yjeA Translation...”
- The Capsule Regulatory Network of Klebsiella pneumoniae Defined by density-TraDISort
Dorman, mBio 2018 - “...-arabinose-phosphoundecaprenol flippase subunit ArnF 1.00 KP1_5178 VK055_3630 arnE SMR family multidrug resistance protein 0.95 KP1_5179 VK055_3628 arnD Polymyxin resistance protein PmrJ 1.00 KP1_5181 VK055_3626 gor Glutathione reductase 1.00 KP1_5206 VK055_3604 wabN Deacetylase 1.00 KP1_5319 VK055_3502 wecA Undecaprenyl-phosphate N-acetylglucosaminyl 1-phosphate transferase 0.98 KP1_0146 VK055_3191 yjeA Translation elongation...”
STM2302 putative inner membrane protein from Salmonella typhimurium LT2
45% identity, 88% coverage
TC 2.A.7.22.2 / P81891 Probable 4-amino-4-deoxy-L-arabinose-phosphoundecaprenol flippase subunit ArnE, component of The undecaprenyl phosphate-α-aminoarabinose flippase ArnE/ArnF heterodimer from the cytoplasm to the periplasm from Salmonella typhi (see 3 papers)
44% identity, 84% coverage
- substrates: Undecaprenyl phosphate-alpha-aminoarabinose
WP_008648542 DMT family transporter from Cupriavidus metallidurans
42% identity, 63% coverage
ARNE_YERPS / Q66A07 Probable 4-amino-4-deoxy-L-arabinose-phosphoundecaprenol flippase subunit ArnE; L-Ara4N-phosphoundecaprenol flippase subunit ArnE; Undecaprenyl phosphate-aminoarabinose flippase subunit ArnE from Yersinia pseudotuberculosis serotype I (strain IP32953) (see paper)
42% identity, 87% coverage
- function: Translocates 4-amino-4-deoxy-L-arabinose-phosphoundecaprenol (alpha-L-Ara4N-phosphoundecaprenol) from the cytoplasmic to the periplasmic side of the inner membrane.
subunit: Heterodimer of ArnE and ArnF. - A novel sequence-based predictor for identifying and characterizing thermophilic proteins using estimated propensity scores of dipeptides.
Charoenkwan, Scientific reports 2021 - “...addition, Fig. 5 depicts three-dimensional structures of TPPs (Q9YFR9, Q57676 and Q9YD25) and non-TPPs (Q8ZDC4, Q66A07 and A1AZ52) having the highest (528.74, 527.79 and 525.29, respectively) and lowest (319.67, 331.20 and 340.61, respectively) TPP scores, respectively. The five top-ranked proteins having the highest TPP scores and...”
- “...Aeropyrum pernix Figure 5 Three-dimensional structures of TPPs (Q9YFR9, Q57676 and Q9YD25) and non-TPPs (Q8ZDC4, Q66A07 and A1AZ52) having the highest (528.74, 527.79 and 525.29, respectively) and lowest (319.67, 331.20 and 340.61, respectively) TPP scores, respectively, where the optimal threshold value is 418. Characterization of thermophilic...”
BTH_I2194 hypothetical protein from Burkholderia thailandensis E264
40% identity, 50% coverage
- A Burkholderia thailandensis DedA Family Membrane Protein Is Required for Proton Motive Force Dependent Lipid A Modification
Panta, Frontiers in microbiology 2020 - “...membrane potential observed in dbcA is responsible for inefficient export of undecaprenyl-P-Ara4N by EmrE-like transporter BTH_I2194 (ArnEF homolog). We reasoned that overexpression of the arn genes in dbcA could compensate colistin hypersensitivity of dbcA . Based on Prokaryotic Operon Database (ProOpDB), putative arn genes in B....”
- “...Another transcriptional unit encodes arn transport gene products- BTH_I2196, BTH_I2195 (23% identity with ArnT), and BTH_I2194 (27% identity with ArnE/ArnF) ( Figure 1A ). Alignments were performed using Needleman-Wunsch alignment ( Altschul et al., 1997 , 2005 ). In our study, we used the plasmid pSC200...”
y1922 hypothetical from Yersinia pestis KIM
42% identity, 83% coverage
BCAL1930 SMR family transporter protein from Burkholderia cenocepacia J2315
40% identity, 50% coverage
- A putative gene cluster for aminoarabinose biosynthesis is essential for Burkholderia cenocepacia viability
Ortega, Journal of bacteriology 2007 - “...to homologues of arnT (pmrK, Ara4N transferase), BCAL1930 (pmrLM, unknown function), arnB (pmrH, UDP-4-ketopentose aminotransferase), arnC (pmrF, Ara4N Und-P...”
- “...transcriptional units (Fig. 1B). One unit comprises arnT and BCAL1930, while the other includes the arn gene loci BCA1A2, BCAL1935, and BCAL1936 (Fig. 1A). This...”
YPO2417 putative membrane protein from Yersinia pestis CO92
42% identity, 87% coverage
BruAb2_0378 hypothetical membrane protein from Brucella abortus biovar 1 str. 9-941
BMI_II847 hypothetical protein from Brucella microti CCM 4915
31% identity, 53% coverage
- Genomic Characterization Provides New Insights for Detailed Phage- Resistant Mechanism for Brucella abortus
Li, Frontiers in microbiology 2019 - “...Outer membrane transporter RD2 158847..159637 791 RD3 376963..382403 4,088 BruAb2_0377 1,335 62.76 % FAD-binding oxidoreductase BruAb2_0378 420 100.00 % Hypothetical protein BruAb2_0379 1,011 100.00 % Epimerase BruAb2_0380 1,455 100.00 % Aminotransferase Deletion 620905..620941 37 BruAb2_0616 1,143 3.25 % Major facilitator family transporter RD4 701096..701938 843 BruAb2_0690...”
- “...present in Bab8416. RD3 contains four genes, BruAb2_0377 to BruAb2_0380 . BruAb2_0377 encodes FAD-binding oxidoreductase. BruAb2_0378 was defined as a hypothetical protein. BruAb2_0379 encodes an epimerase that catalyzes the transformation of dTDP-glucose to dTDP-4-oxo-6-deoxy- D -glucose. BruAb2_0380 encodes an amino transferase that participates in arginine and...”
- Comparative Genome-Wide Transcriptome Analysis of Brucella suis and Brucella microti Under Acid Stress at pH 4.5: Cold Shock Protein CspA and Dps Are Associated With Acid Resistance of B. microti
de, Frontiers in microbiology 2021 - “...macrophages. Fourteen of the mutants, affected in the genes BMI_I1066, BMI_II893, BMI_I1677, BMI_II226, BMI_II385, BMI_II460, BMI_II847, BMI_I1652, BMI_I1679, BMI_I733, BMI_I686, BMI_II580, BMI_II225, and BMI_II898, did not show any reduction in survival as compared to the wild-type strain in minimal medium at pH 4.5 over an incubation...”
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