PaperBLAST

PaperBLAST Hits for VIMSS81829 conserved hypothetical protein (239 a.a., MSVSRRDVLK...)

Show query sequence

>VIMSS81829 conserved hypothetical protein
MSVSRRDVLKFATVTPGLLGLGVAAAALCAVPASTAGSLGTLLDYAAGVIPASQIRATGA
VGAIRYVSDPRGTWAVGKPIQVTEARDLINNGLKIVSCYQYGKGNTADWLGGATAGLRHA
QRGVQLHTAAGGPVSAPIYASIDSNPTYEQYKQQVAPYLRSWESVIGHQRTGVYANSRTI
AWALQDGLASYFWQHNWGSPKGYTHPAANLHQVEIDRRTVGGVGVDVNTILKPQFGQWA

Running BLASTp...

Found 10 similar proteins in the literature:

ML1190 conserved hypothetical protein from Mycobacterium leprae TN
100% identity, 100% coverage

• Inactivation of Rv2525c, a substrate of the twin arginine translocation (Tat) system of Mycobacterium tuberculosis, increases beta-lactam susceptibility and virulence
  Saint-Joanis, Journal of bacteriology 2006
  • “...of M. leprae, only one of the corresponding genes, ml1190, escaped inactivation; it is orthologous to the rv2525c gene of M. tuberculosis. The conservation of...”
  • “...C precursor NF plcA Phospholipase C precursor ml1190 Unknown ml0497 ps Similar to G755244 acid phosphatase del ugpB sn-Glycerol-3-phosphate transport del...”

LYS25_MYCTU / I6XEI5 Putative peptidoglycan hydrolase Rv2525c; EC 3.2.1.17 from Mycobacterium tuberculosis (strain ATCC 25618 / H37Rv) (see 2 papers)
NP_217041 hypothetical protein from Mycobacterium tuberculosis H37Rv
Rv2525c hypothetical protein from Mycobacterium tuberculosis H37Rv
JTY_RS13125 DUF1906 domain-containing protein from Mycobacterium tuberculosis variant bovis BCG str. Tokyo 172
82% identity, 100% coverage

• function: May function as a peptidoglycan hydrolase with glycosidase activity (PubMed:25260828). In vitro, displays esterase activity toward p-nitrophenyl esters of various acyl chain length (C4 to C16), with a preference for p-nitrophenyl butyrate (C4) (PubMed:25869294).
  catalytic activity: Hydrolysis of (1->4)-beta-linkages between N-acetylmuramic acid and N-acetyl-D-glucosamine residues in a peptidoglycan and between N-acetyl-D-glucosamine residues in chitodextrins.
  disruption phenotype: Cells lacking this gene display an increase in susceptibility to some beta-lactam antibiotics and, despite slower growth in vitro, enhanced virulence in both cellular and murine models of tuberculosis. No detectable difference in the lipid profiles.
• Expression, Purification and Characterisation of Secreted Esterase Rv2525c from Mycobacterium tuberculosis.
  Dang, Applied biochemistry and biotechnology 2015 (PubMed)
  • GeneRIF: Expression, Purification and Characterisation of Secreted Esterase Rv2525c from Mycobacterium tuberculosis.
• Inactivation of Rv2525c, a substrate of the twin arginine translocation (Tat) system of Mycobacterium tuberculosis, increases beta-lactam susceptibility and virulence.
  Saint-Joanis, Journal of bacteriology 2006
  • GeneRIF: Upon exposure to antituberculous drugs, rv2525c expression is significantly up-regulated together with those of other genes involved in cell wall biogenesis
• Mycobacterium tuberculosis Gene Expression Associated With Fluoroquinolone Resistance and Efflux Pump Inhibition
  van, The Journal of infectious diseases 2023
  • “....002 -1.33 .45 Rv1819c -1.85 .004 -1.49 .13 eQTL Analysis Rv2525c -1.82 .004 -1.20 .84 Rv3500c -1.86 .01 -1.65 .03 Rv1522c -1.76 .01 -1.39 .28 Rv0191 +1.64 .01...”
• MtrA modulates Mycobacterium tuberculosis cell division in host microenvironments to mediate intrinsic resistance and drug tolerance
  Peterson, Cell reports 2023
  • “...encode proteins with PG hydrolase activity: ami1 , ripA , ripB , ripD , and Rv2525c . PG hydrolases are present in multiple variant forms in all bacteria, where their activities are harnessed to support cell growth, division, and differentiation, enabling bacteria to propagate and adapt...”
  • “...a non-catalytic PG-binding function. 69 Finally, structural studies suggest a PG glycoside hydrolase function for Rv2525c, although its activity has not been established. 70 To assess the effect of MtrA regulation on these PG cleavage enzymes and the impact on Mtb cell division and growth, we...”
• Phosphorylation of CFP10 modulates Mycobacterium tuberculosis virulence
  Malakar, mBio 2023
  • “...the twin-arginine motif in the signal sequence ( 17 ). Four phospholipase C enzymes and Rv2525c, a conserved hypothetical protein, are known Tat substrates ( 17 , 18 ) in mycobacteria. In addition to the classical Sec and Tat secretion system, most Gram-negative bacteria are equipped...”
• Rv0500A is a transcription factor that links Mycobacterium tuberculosis environmental response with division and impacts host colonization
  Kevorkian, Molecular microbiology 2022
  • “...ripB , ripD , erp (exported repetitive protein, also known as pirG ), lcp1 , rv2525c , and rv2864c ( Figure 2c , d , Tables S4 and S5 ) ( Bellinzoni et al., 2014 ; Berthet et al., 1998 ; Bth et al., 2011 ;...”
  • “...2014 ) Structural studies suggest a peptidoglycan hydrolase function for the mycobacterium tuberculosis tat-secreted protein Rv2525c . Journal of Structural Biology , 188 , 156 164 . 25260828 Berthet FX , Lagranderie M , Gounon P , Laurent-Winter C , Ensergueix D , Chavarot P (...”
• Genome-Wide Study of Drug Resistant Mycobacterium tuberculosis and Its Intra-Host Evolution during Treatment
  Lagutkin, Microorganisms 2022
  • “...a duplication of this repetitive region. Rv1435c was shown to be a part of an Rv2525c -coregulated gene cluster, which consists of cell wall synthesis proteins and penicillin-binding proteins. It was demonstrated that this cluster is upregulated in INH- and ETH-treated MTB [ 66 ]. In...”
  • “...B. Demangel C. Jackson M. Brodin P. Marsollier L. Boshoff H. Cole S.T. Inactivation of Rv2525c, a substrate of the twin arginine translocation (Tat) system of Mycobacterium tuberculosis , increases -Lactam susceptibility and virulence J. Bacteriol. 2006 188 6669 6679 10.1128/JB.00631-06 16952959 67. Chen J. Zhang...”
• Computational identification of significant immunogenic epitopes of the putative outer membrane proteins from Mycobacterium tuberculosis
  Sundar, Journal, genetic engineering & biotechnology 2021
  • “...membrane proteins of Mtb. Among these, certain immunodominant epitopes of Rv0172, Rv0295c, Rv1006, Rv2264c, and Rv2525c were found, which are capable of binding B-cell and a maximum number of MHC alleles. The selected immunodominant epitopes were screened for their allergenic and antigenic properties, their percentage identity...”
  • “...27 0.7743 1.00823 52.17% 16 Rv2307c 115 135 GYGGNPGRPSEQGLAADARAA 12 2 0.9422 0.7492 64.71% 17 Rv2525c a 102 153 YGKGSTADWLGGASAGVQHARRGSELHAAAGGPTSAPIYASIDDNPSYEQYK 27 27 0.9026 0.48836 No significant similarity found 18 Rv2672 33 72 AFGADPRFATYSGAGPQGAATTTPPPAGPPPLAAPKNDLS 21 27 0.7615 0.65308 69.23% 19 Rv2891 33 52 PAHADDSRLGWPLRPPPAVV 21 4 1.2467...”
• Structure-Aware Mycobacterium tuberculosis Functional Annotation Uncloaks Resistance, Metabolic, and Virulence Genes
  Modlin, mSystems 2021
  • “...protein Probable antitoxin VapB/antigen 28066388, 23140854 Rv2272 Transmembrane protein Probable gamma delta T-cell activator 23389928 Rv2525c Tat pathway signal sequence Probable peptidoglycan hydrolase 16952959, 25869294, 25260828 Rv2923c Hypothetical protein Probable osmotically induced bacterial protein C (OsmC, a probable peroxide reductase) 22088319 Rv3632 Membrane protein Putative flippase...”
• The prominent alteration in transcriptome and metabolome of Mycobacterium bovis BCG str. Tokyo 172 induced by vitamin B₁
  Song, BMC microbiology 2019
  • “...genes, JTY_RS12370 ( Rv2390c ), JTY_RS00960 ( Rv0179c ), JTY_RS08085 ( Rv1535 ), JTY_RS13125 ( Rv2525c ) and JTY_RS09350 ( Rv1799 ) were upregulated more than 2-fold (Additional file 2 : Table S2). Universal stress protein There are 10 universal stress proteins (ups) in M. tuberculosis...”
• More
• The prominent alteration in transcriptome and metabolome of Mycobacterium bovis BCG str. Tokyo 172 induced by vitamin B₁
  Song, BMC microbiology 2019
  • “...to those genes, JTY_RS12370 ( Rv2390c ), JTY_RS00960 ( Rv0179c ), JTY_RS08085 ( Rv1535 ), JTY_RS13125 ( Rv2525c ) and JTY_RS09350 ( Rv1799 ) were upregulated more than 2-fold (Additional file 2 : Table S2). Universal stress protein There are 10 universal stress proteins (ups) in...”

MAP2334c hypothetical protein from Mycobacterium avium subsp. paratuberculosis str. k10
80% identity, 99% coverage

• Inactivation of Rv2525c, a substrate of the twin arginine translocation (Tat) system of Mycobacterium tuberculosis, increases beta-lactam susceptibility and virulence
  Saint-Joanis, Journal of bacteriology 2006
  • “...Rv2525c; M. tuberculosis; ML1190, M. leprae; MAP2334c, Mycobacterium avium subsp. paratuberculosis; nfa47650, Nocardia farcinica. Stars denote identical...”

MAB_1511 hypothetical protein from Mycobacterium abscessus ATCC 19977
65% identity, 100% coverage

• Mycobacterium abscessus extracellular vesicles increase mycobacterial resistance to clarithromycin in vitro
  Vermeire, Proteomics 2024 (secret)

nfa47650 hypothetical protein from Nocardia farcinica IFM 10152
60% identity, 84% coverage

• Inactivation of Rv2525c, a substrate of the twin arginine translocation (Tat) system of Mycobacterium tuberculosis, increases beta-lactam susceptibility and virulence
  Saint-Joanis, Journal of bacteriology 2006
  • “...leprae; MAP2334c, Mycobacterium avium subsp. paratuberculosis; nfa47650, Nocardia farcinica. Stars denote identical residues; periods and colons indicate...”

cg0955 hypothetical protein from Corynebacterium glutamicum ATCC 13032
45% identity, 85% coverage

• The Iron Deficiency Response of Corynebacterium glutamicum and a Link to Thiamine Biosynthesis
  Küberl, Applied and environmental microbiology 2020 (secret)
• Corynebacterium glutamicum possesses β-N-acetylglucosaminidase
  Matano, BMC microbiology 2016 (no snippet)
• The DtxR protein acting as dual transcriptional regulator directs a global regulatory network involved in iron metabolism of Corynebacterium glutamicum
  Brune, BMC genomics 2006
  • “...28 n.d. +1010 cg0470 - TTAGGTTAAGCTAATCTAG 32 n.d. +978 cg0591 - TTAGTAAAGGCTCACCTAA 91 n.d. +310 cg0955 - TTACGTGAGCGTAGCCGAA 200 n.d. +2.8 cg1642 - TTAGGTTAGGCAAGCCATA 39 n.d. +4.4 cg3247 cgtR11 ATCAGTAAGGCTAGACTAA 87 n.d. +5.5 cg3394 - TTAAGGTAAGTTCAGCTAA 37 n.d. +4.6 cg1070 - ATAGGTTATCCAAGCCTAA 18 n.d. n.d. cg1088...”
  • “...CE0881 TTAGGTACCCTAACCTCAC CE08820884 iron ABC transport system cg0926 , JK1887 CE0912 GTAGGTTACGCGAACGTAG - hypothetical protein cg0955 CE1009 TTAGGCATCCCTTGCCTCG CE1010 hypothetical proteins DIP0894 CE1346 AGAGTGTAGGCTTACCTAT - hypothetical protein cg1405 CE1860 TTAGGTTATAGTTTCCTTT CE1859 hypothetical proteins - CE1917 GTGGGTGAGGCAAGCCTAA - phage integrase/recombinase - CE1940 TGAAGTAACACTACCCTAA - cation transporting P-type...”

CgS9114_13715 DUF1906 domain-containing protein from Corynebacterium glutamicum S9114
cgR_0949 hypothetical protein from Corynebacterium glutamicum R
44% identity, 85% coverage

• Proteome analysis guided genetic engineering of Corynebacterium glutamicum S9114 for tween 40-triggered improvement in L-ornithine production
  Jiang, Microbial cell factories 2020
  • “...Putative esterase 3.378 3.5667E05 Down 33.531 UPI0002231962 CgS9114_04952 Putative esterase 3.401 2.0229E08 Down 39.62 UPI000133536B CgS9114_13715 Putative secreted protein 3.413 2.1044E08 Down 29.955 UPI000133510C CgS9114_14352 Hypothetical protein 3.521 0.00018473 Down 24.492 UPI0001335576 CgS9114_00220 Ferredoxin-NADP+ reductase 3.597 5.1049E07 Down 50.056 UPI000223193A CgS9114_01878 protein prenyltransferase 3.774 6.0916E07 Down...”
• Cellulosic hydrocarbons production by engineering dual synthesis pathways in Corynebacterium glutamicum
  Xu, Biotechnology for biofuels and bioproducts 2022
  • “...ado-rbs-aar , and pH36- ado- TacM -aar . The signal peptide sequences of Ncgl1289 and cgR_0949 were amplified from C. glutamicum ATCC 13032 and C. glutamicum S9114. Then the signal peptide sequences of Ncgl1289 and the fragment of oleT JE gene were overlapped together and inserted...”
• Corynebacterium glutamicum possesses β-N-acetylglucosaminidase
  Matano, BMC microbiology 2016 (no snippet)
• Construction of a novel twin-arginine translocation (Tat)-dependent type expression vector for secretory production of heterologous proteins in Corynebacterium glutamicum
  Zhang, Plasmid 2015 (PubMed)
  • “...RBS sequence for protein translation, and the strong cgR_0949 signal sequence for protein secretion via the Tat pathway in C. glutamicum. The applicability of...”
  • “...Tat-type signal peptides from <ce:italic>C. glutamicum</ce:italic>, CgR_0949 is the strongest signal sequence that mediates protein secretion (<ce:cross-refs...”
• Influence of SigB inactivation on Corynebacterium glutamicum protein secretion
  Watanabe, Applied microbiology and biotechnology 2013 (PubMed)
  • “...Utilizing a signal peptide derived from C. glutamicum R CgR_0949, a sigB disruption mutant able to secrete 3- to 5-fold more green fluorescence protein (GFP)...”
  • “...GFP productivity reported in C. glutamicum to date. CgR_0949 signal sequence length (30 residues), type (Tat) or the target protein identity (GFP or -amylase)...”

CE0912 conserved hypothetical protein from Corynebacterium efficiens YS-314
49% identity, 68% coverage

• The DtxR protein acting as dual transcriptional regulator directs a global regulatory network involved in iron metabolism of Corynebacterium glutamicum
  Brune, BMC genomics 2006
  • “...iron ABC transport system cg0771 CE0881 TTAGGTACCCTAACCTCAC CE08820884 iron ABC transport system cg0926 , JK1887 CE0912 GTAGGTTACGCGAACGTAG - hypothetical protein cg0955 CE1009 TTAGGCATCCCTTGCCTCG CE1010 hypothetical proteins DIP0894 CE1346 AGAGTGTAGGCTTACCTAT - hypothetical protein cg1405 CE1860 TTAGGTTATAGTTTCCTTT CE1859 hypothetical proteins - CE1917 GTGGGTGAGGCAAGCCTAA - phage integrase/recombinase - CE1940...”

DIP0793 Putative secreted protein from Corynebacterium diphtheriae NCTC 13129
42% identity, 78% coverage

• Adherence and invasive properties of Corynebacterium diphtheriae strains correlates with the predicted membrane-associated and secreted proteome
  Sangal, BMC genomics 2015
  • “...copper-binding protein. Both of the non-lipoprotein Tat substrates contain domains of unknown function, of which DIP0793 contains a PF08924 (BacA-like) putative peptidoglycan hydrolase domain. In addition to the Sec and Tat translocase, a single type VII secretion system was identified in the C. diphtheriae core proteome,...”

MAB_4801 Possible twin-arginine translocation pathway from Mycobacterium abscessus ATCC 19977
38% identity, 87% coverage

• Mycobacterium abscessus extracellular vesicles increase mycobacterial resistance to clarithromycin in vitro
  Vermeire, Proteomics 2024 (secret)

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Statistics

How It Works

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.

Secrets

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.

Omissions from the PaperBLAST Database

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.