PaperBLAST
PaperBLAST Hits for VIMSS14605 conserved inner membrane protein (125 a.a., MQRIILIIIG...)
Show query sequence
>VIMSS14605 conserved inner membrane protein
MQRIILIIIGWLAVVLGTLGVVLPVLPTTPFILLAAWCFARSSPRFHAWLLYRSWFGSYL
RFWQKHHAMPRGVKPRAILLILLTFAISLWFVQMPWVRIMLLVILACLLFYMWRIPVIDE
KQEKH
Running BLASTp...
Found 19 similar proteins in the literature:
YbaN / b0468 DUF454 domain-containing inner membrane protein YbaN from Escherichia coli K-12 substr. MG1655 (see 2 papers)
b0468 conserved inner membrane protein from Escherichia coli str. K-12 substr. MG1655
Z0585 putative gene 58 from Escherichia coli O157:H7 EDL933
SF5M90T_438 DUF454 family protein from Shigella flexneri 5a str. M90T
100% identity, 100% coverage
- COLOMBOS: access port for cross-platform bacterial expression compendia
Engelen, PloS one 2011 - “...Fur, NrdR b4291 fecA Fe 3+ dicitrate transport protein fecABCDE + + Fur, CRP, PdhR b0468 ybaN Inner membrane protein ybaN + Predicted b0804 ybiX PKHD-type hydroxylase ybiX + Predicted; Fur dependent expression b1018 efeO UPF0409 protein efeUOB + Predicted; functional in related strain b1452 yncE...”
- A divalent ion is crucial in the structure and dominant-negative function of ID proteins, a class of helix-loop-helix transcription regulators
Wong, PloS one 2012 - “...constructs for expression and crystallization ID2 HLH (residues 2482) was cloned from full-length cDNA (Genecopoeia, Z0585) using Gateway (Invitrogen) as per manufacturer's instructions, into the pDONR221 vector (Invitrogen). Due to known instability issues of ID2, a C-terminal 14 amino acid long polypeptide (LKPSFLVQSGDIAS) was included to...”
- RNA-seq analysis of the influence of anaerobiosis and FNR on Shigella flexneri
Vergara-Irigaray, BMC genomics 2014 - “...hypothetical protein 0.81 SF5M90T_479 ybbF conserved hypothetical protein -1.19 SF5M90T_2195 rtn conserved hypothetical protein -1.50 SF5M90T_438 ybaN conserved hypothetical protein -1.73 SF5M90T_1853 conserved hypothetical protein -2.03 -2.58 SF5M90T_1647 conserved hypothetical protein -2.11 SF5M90T_983 ymcD conserved hypothetical protein -2.34 SF5M90T_4094 yjbA P-starvation inducible protein PsiE -2.51 1.69...”
SEET0819_09365, STM14_0567 DUF454 family protein from Salmonella enterica subsp. enterica serovar Typhimurium str. 14028S
84% identity, 100% coverage
VC1052 conserved hypothetical protein from Vibrio cholerae O1 biovar eltor str. N16961
Q9KT53 Inner membrane protein from Vibrio cholerae serotype O1 (strain ATCC 39315 / El Tor Inaba N16961)
44% identity, 93% coverage
- Preclinical evaluation of Vaxfectin-adjuvanted Vero cell-derived seasonal split and pandemic whole virus influenza vaccines
Smith, Human vaccines & immunotherapeutics 2013 - “...mixture of cationic lipid VC1052 and neutral co-lipid DPyPE. VC1052 [()-N-(3aminopropyl)-N,N-dimethyl-2,3-bis(cis-9-tetradecenyloxy)1-propanaminium bromide] was...”
- “...lipid film from an equimolar chloroform solution of VC1052 and DPyPE in glass vials containing FluroTec(R) stoppers. The chloroform was evaporated under a...”
- PhoB regulates motility, biofilms, and cyclic di-GMP in Vibrio cholerae
Pratt, Journal of bacteriology 2009 - “...VC0724 VC0725 VC0826 VC0829 VC0831 VC1067 VC0034 VC0948 VC1052 VC1301 VC2053 VCA0079 VCA1050 Gene name 6635 6636 PRATT ET AL. J. BACTERIOL. Downloaded from...”
- Comprehensive in silico analyses of fifty-one uncharacterized proteins from Vibrio cholerae
Basu, PloS one 2024 - “...Furthermore, among the 51 proteins, a total of 10 proteins (Uniprot ID-Q9KKX0, Q9KVJ9, Q9KP29, Q9KPA3, Q9KT53, Q9KL56, Q9KRE6, Q9K2J6, Q9KVW5, and Q9KPZ1) have been determined to be insoluble in their natural state. A total of 15 positively charged proteins (rich in Arginine and Lysine) and 24...”
- “...Q9KND3 Q9KLQ3 Q9KSV6 Q9KND3 Q9KND3 Q9KND3 Q9KP29 Q9KKS6 Q9KND3 Q9KPA3 Q9KPA3 Q9KPA3 Q9KMX1 Q9KU58 Q9KPA3 Q9KT53 Q9KT53 Q9KT53 Q9KPD6 BIBIN2 Q9KT53 Q9KRE6 Q9KRE6 Q9KRE6 Q9KNF4 Q9K2J6 Q9KRE6 Q9KKS6 Q9KKS6 Q9KKS6 Q9KL56 Q9KS64 Q9KKS6 Q9KN87 Q9KN87 Q9KN87 Q9KLX2 Q9KN40 Q9KN87 Q9KU58 Q9KU58 Q9KU58 Q9KLQ3 Q9KL81 Q9KU58 Q9KPP0...”
BUE60_21160 YbaN family protein from Pseudomonas syringae pv. actinidiae
40% identity, 84% coverage
BQ00830 hypothetical protein from Bartonella quintana str. Toulouse
51% identity, 60% coverage
- Bartonella quintana deploys host and vector temperature-specific transcriptomes
Abromaitis, PloS one 2013 - “...1.41 0.02 5.35 1.59 7 2.68 BQ00240 thioredoxin trxA 0.68 0.71 1.28 1.79 2 2.60 BQ00830 hypothetical protein 0.82 0.53 0 2.09 2 2.56 BQ07681 hypothetical protein 0.70 0.58 0 2.11 3 2.43 BQ11010 hypothetical protein 0.92 0.32 0 1.92 1 2.36 BQ09250 cold shock protein...”
- “...8.50E-71 306837668 BQ00570 LysM domain/BON superfamily protein 2.00E-52 EHH06667.1 LysM domain/BON superfamily protein 3.00E-47 325291490 BQ00830 - - - inner membrane protein ybaN 1.70E-23 358048936 BQ02770 XRE family transcriptional regulator 4.00E-08 YP_002004972.1 conserved hypothetical protein Bartonella sp. AR 15-3 3.90E-09 319405804 BQ05030 glycosyl transferase family protein...”
Rmet_0221 YbaN family protein from Cupriavidus metallidurans CH34
41% identity, 74% coverage
- Phenotypic and Genetic Characterization of Temperature-Induced Mutagenesis and Mortality in Cupriavidus metallidurans
Van, Frontiers in microbiology 2021 - “...-derivative of CH34 This study CH34-Km R CH34 harboring a EZ-Tn5 < KAN 2> in Rmet_0221 coding for a conserved hypothetical protein, Km R This study CH34 1009 CH34 Rmet_1009:: tet , Tc R This study CH34-TIMM R1 1009 CH34-TIMM R1 Rmet_1009:: tet , Tc R...”
- “...C. metallidurans CH34 strain, i.e., CH34-Km R , containing a kanamycin resistance cassette in gene Rmet_0221, coding for a hypothetical protein, was used in the competition assays. The different strains, i.e., CH34-TIMM R1 , CH34-TIMM R2 , CH34 and CH34-Km R ( Table 1 ), were...”
SAOUHSC_00131 hypothetical protein from Staphylococcus aureus subsp. aureus NCTC 8325
SA0161 hypothetical protein from Staphylococcus aureus subsp. aureus N315
NWMN_0112 hypothetical protein from Staphylococcus aureus subsp. aureus str. Newman
35% identity, 96% coverage
- Transcriptomic analyses reveal the potential antibacterial mechanism of citral against Staphylococcus aureus
Liao, Frontiers in microbiology 2023 - “...ferrochelatase SAOUHSC_02681 5.770892267 8.0905E-128 nitrate reductase subunit alpha SAOUHSC_02680 5.655444057 1.3733E-110 nitrate reductase subunit beta SAOUHSC_00131 5.423736733 3.31075E-51 YbaN family protein SAOUHSC_02679 5.263068749 3.38926E-75 respiratory nitrate reductase subunit delta SAOUHSC_02645 5.222935859 2.92178E-05 LytTR family DNA-binding domain-containing protein 3.2.3. Go functional enrichment analysis GO enrichment analysis was...”
- Haem-iron plays a key role in the regulation of the Ess/type VII secretion system of Staphylococcus aureus RN6390
Casabona, Microbiology (Reading, England) 2017 - “...isdI 5.7 Haem-degrading monooxygenase IsdI SAOUHSC_01086 isdF 6.1 ABC permease IsdF Fur [ 65 ] SAOUHSC_00131 6.1 Putative membrane spanning protein SAOUHSC_01088 srtB 6.2 Sortase SrtB Fur [ 65 ] SAOUHSC_01084 isdD 6.2 ATP-hydrolysing and haem-binding protein IsdD Fur [ 65 ] SAOUHSC_02432 6.2 Unknown, hypothetical...”
- Functional analysis of the EsaB component of the Staphylococcus aureus Type VII secretion system
Casabona, Microbiology (Reading, England) 2017 - “...protein FhuA 7.0 SAOUHSC_00071 sirC 5.3 Involved in staphyloferrin B transport into the cytoplasm 4.6 SAOUHSC_00131 5.3 Putative membrane protein 6.1 SAOUHSC_02821 5.8 Putative membrane protein ns SAOUHSC_02719 6.2 ABC transporter ATP-binding protein 5.5 SAOUHSC_01920 6.3 Putative lipoprotein ns SAOUHSC_02428 htsB 6.3 Heme transport system permease...”
- Characterizing the effects of inorganic acid and alkaline shock on the Staphylococcus aureus transcriptome and messenger RNA turnover
Anderson, FEMS immunology and medical microbiology 2010 - “...family protein Unkown function sa_c2968s2524_a_at 3.3 ND 2.5 SA0156 hypothetical protein sa_c3224s2774_a_at 7.8 2.5 2.5 SA0161 hypothetical protein sa_c6700s5841_a_at 2.1 2.5 2.5 SA0259 hypothetical protein sa_c7203s6269_a_at 6.5 ND 2.5 SA0445 hypothetical protein sa_c7760s6763_at * 23.5 15 30 SA0625 hypothetical protein sa_c8897s7814_a_at 6.5 ND 2.5 SA0692 hypothetical...”
- Characterization of the Staphylococcus aureus heat shock, cold shock, stringent, and SOS responses and their effects on log-phase mRNA turnover
Anderson, Journal of bacteriology 2006 - “...putative MSSA476-SAS070 N315-SA0413 N315-SA0751 N315-SA1186 N315-SA2496 SA0161 SA0299 SA0436 SA0448 SA0497 SA0537 SA0692 SA1033 SA1372 SA1375 SA1438 SA1524...”
- “...N315-SA1777 N315-SA1832 N315-SA2299 N315-SA0326 N315-SA0551 N315-SA1829 SA0161 SA0191 SA0215 SA0252 SA0255 SA0259 SA0314 SA0436 SA0568 SA0625 SA0641 SA0814...”
- Fur regulation of Staphylococcus aureus heme oxygenases is required for heme homeostasis
Lojek, International journal of medical microbiology : IJMM 2018 - “...isdCDEFsrtBisdG operons. The endogenous promoter for isdI was defined as the intergenic region between orfX (NWMN_0112) and aldA (NWMN_0113). However, the Fur box for isdI jis contained within the 3 region of the orfX operon, and this region was also included in the constructed promoter for...”
- Induction of virulence gene expression in Staphylococcus aureus by pulmonary surfactant
Ishii, Infection and immunity 2014 - “...California, Berkeley Gene no. NWMN_0093 NWMN_0095 NWMN_0112 NWMN_0207 NWMN_0221 NWMN_0223 NWMN_0224 NWMN_0225 NWMN_0232 NWMN_0233 NWMN_0245 NWMN_0246 NWMN_0360...”
HD1939 conserved hypothetical protein from Haemophilus ducreyi 35000HP
41% identity, 84% coverage
Smlt3895 putative transmembrane protein from Stenotrophomonas maltophilia K279a
44% identity, 63% coverage
- HemU and TonB1 contribute to hemin acquisition in Stenotrophomonas maltophilia
Liao, Frontiers in cellular and infection microbiology 2024 - “...degradation of hemin to produce biliverdin, ferrous iron, and carbon monoxide. The protein encoded by Smlt3895 was predicted to be a 155-aa inner membrane transmembrane protein and displayed no significant similarity with the proteins of known functions. The proteins encoded by Smlt3894 , Smlt3893 , and...”
DIP2356 Putative conserved membrane protein from Corynebacterium diphtheriae NCTC 13129
49% identity, 52% coverage
APL_1806 hypothetical protein from Actinobacillus pleuropneumoniae L20
36% identity, 86% coverage
ACICU_RS04605, DMO12_RS04720 YbaN family protein from Acinetobacter baumannii ACICU
ACICU_00880 hypothetical protein from Acinetobacter baumannii ACICU
32% identity, 76% coverage
- Genomics of Acinetobacter baumannii iron uptake
Artuso, Microbial genomics 2023 - “...hphA DMO12_RS04700 Slam-dependent haemophore hsmA DMO12_RS04705 Hemophilin secretion modulator DMO12_RS04710 TonB-related protein DMO12_RS04715 Haem oxygenase DMO12_RS04720 Hypothetical protein basJ DMO12_RS13105 Acinetobactin biosynthesis isochorismate synthase basI DMO12_RS13110 Acinetobactin biosynthesis phosphopantetheinyl transferase basH DMO12_RS13115 Acinetobactin biosynthesis thioesterase barB DMO12_RS13120 Acinetobactin export ABC transporter permease/ATP-binding subunit barA DMO12_RS13125 Acinetobactin...”
- Chromosome Architecture and Gene Content of the Emergent Pathogen Acinetobacter haemolyticus
Castro-Jaimes, Frontiers in microbiology 2020 - “...spot 6 in the representative strains, and two of them had recombination signals (ACICU_RS04580 and ACICU_RS04605). All these data showed that A. haemolyticus can uptake hemin for iron acquisition and that the gene clusters had been integrated via recombination with neighboring genes. Regarding virulence factors characterized...”
- New Shuttle Vectors for Gene Cloning and Expression in Multidrug-Resistant Acinetobacter Species
Lucidi, Antimicrobial agents and chemotherapy 2018 - “...baumannii ACICU gene cluster from the ACICU_00873 to ACICU_00880 genes) directly into pVRL1 (data not shown), supporting the potential of this plasmid in...”
- Antimicrobial Activity of Gallium Compounds on ESKAPE Pathogens
Hijazi, Frontiers in cellular and infection microbiology 2018 - “...bp DNA fragment encompassing eight genes of the hemO cluster of ACICU (from ACICU_00873 to ACICU_00880 locus) was obtained by PCR amplification using primers HemO_FW (5-CATTTGGTTTCCGAGTCTCG-3) and HemO_RV (5-CCATGATGCGTACCATGCA-3). The PCR product was purified by the PCR Clean-Up System (Promega) and blunt-end ligated to the SmaI...”
ABLAC_16850 YbaN family protein from Acinetobacter baumannii LAC-4
32% identity, 76% coverage
SH1866 hypothetical protein from Staphylococcus haemolyticus JCSC1435
31% identity, 96% coverage
PP1004 conserved hypothetical protein from Pseudomonas putida KT2440
33% identity, 85% coverage
SMLT_RS19415 YbaN family protein from Stenotrophomonas maltophilia K279a
33% identity, 77% coverage
- Putative Iron Acquisition Systems in Stenotrophomonas maltophilia
Kalidasan, Molecules (Basel, Switzerland) 2018 - “...Heme ABC transporter, ATPase component SMLT_RS11325 99% (K279a) Hyp1 Hypothetical protein related to heme utilization SMLT_RS19415 98% (1337) HmuU Heme ABC transporter, permease protein SMLT_RS11320 92% (K279a) HmuT Heme ABC transporter, cell surface heme and hemoprotein receptor SMLT_RS11315 97% (D457) Subsystem: Heme, hemin uptake and utilization...”
SPO0005 YbaN family protein from Ruegeria pomeroyi DSS-3
42% identity, 86% coverage
Dshi_1454 hypothetical protein from Dinoroseobacter shibae DFL 12
31% identity, 70% coverage
SMb20557 CONSERVED HYPOTHETICAL PROTEIN from Sinorhizobium meliloti 1021
48% identity, 72% coverage
For advice on how to use these tools together, see
Interactive tools for functional annotation of bacterial genomes.
The PaperBLAST database links 789,361 different protein sequences to 1,256,019 scientific articles. Searches against EuropePMC were last performed on January 10 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