PaperBLAST

PaperBLAST Hits for EX31_RS24375 (84 a.a., MDRNDEVIQT...)

Show query sequence

>EX31_RS24375
MDRNDEVIQTHPLVGWDISTVDSYDAMMIRLHYLSSKDQTPEDAQVDRTLWLTTDVARQL
INILEAGIEKIESNEYEYSDHRKH

Running BLASTp...

Found 10 similar proteins in the literature:

G4234_05420 biofilm formation regulator BssS from Serratia marcescens
87% identity, 100% coverage

• Whole genome sequence of Serratia marcescens 39_H1, a potential hydrolytic and acidogenic strain
  Obi, Biotechnology reports (Amsterdam, Netherlands) 2020
  • “...abiotic stress conditions and these genes were identified in 39_H1 as biofilm formation regulator genes (G4234_05420; G4234_20990) [ 37 , 38 ]. Chitinases (G4234_01750; G4234_14125) control phytopathogens that affect plant health [ 39 ]. The above mentioned attributes confirms the relevance of strain 39_H1 in agriculture....”

NJ56_16600 biofilm formation regulator BssS from Yersinia ruckeri
86% identity, 100% coverage

• Genome Sequence of the Fish Pathogen Yersinia ruckeri SC09 Provides Insights into Niche Adaptation and Pathogenic Mechanism
  Liu, International journal of molecular sciences 2016
  • “...NJ56_16305 NJ56_16310 baeS baeR Multidrug efflux NJ56_15220 NJ56_15210 rcsC rcsD Capsular polysaccharide synthesis NJ56_10345 rcsF NJ56_16600 NJ56_16590 qseE qseF Attaching and effacing lesions NJ56_11950 rpoN NJ56_13445 NJ56_13450 uhpB uhpA Hexose phosphate transport NJ56_14760 NJ56_14755 uhpB uhpA NJ56_14595 NJ56_14570 cheA cheB Bacterial chemotaxis NJ56_14565 cheY NJ56_15775 NJ56_15780...”

CH1034_180150 biofilm formation regulator BssS from Klebsiella pneumoniae
67% identity, 100% coverage

• Transcriptional profiling of Klebsiella pneumoniae defines signatures for planktonic, sessile and biofilm-dispersed cells
  Guilhen, BMC genomics 2016
  • “...11.37 2.19 26.02 17.63 3 CH1034_220103 yncC MFS transporter 634.15 478.67 84.96 713.34 340.06 1 CH1034_180150 bssS biofilm regulator 24731.65 10960.85 1747.59 16844.60 10452.60 1 CH1034_250228 yejG hypothetical protein 11084.19 4607.89 407.32 6588.61 5798.71 1 13h-old biofilm CH1034_220106 yidP Transcriptional regulator, GntR family protein 109.08 208.43...”

SGP1_RS09085 biofilm formation regulator BssS from Sodalis glossinidius str. 'morsitans'
74% identity, 100% coverage

• The holobiont transcriptome of teneral tsetse fly species of varying vector competence
  Medina, BMC genomics 2021
  • “...For example, orthologs of type II toxin-antitoxin systems (SGP1_RS14115) along with a formation regulator BssS (SGP1_RS09085) facilitate biofilm formation [ 61 , 62 ]; hypothetically this may support close proximity of Sodalis to the PM lining of the gut lumen, where the bacterium may then deploy...”

KPK_3485 hypothetical protein from Klebsiella pneumoniae 342
67% identity, 100% coverage

• Elucidating the regulon of multidrug resistance regulator RarA in Klebsiella pneumoniae
  De, Antimicrobial agents and chemotherapy 2013
  • “...downregulation of both KPN_02212 narJ (nitrate reductase) and KPK_3485 nirD (nitrite reductase), which are involved in the reduction of nitrate or nitrite to...”

STM1161 putative cytoplasmic protein from Salmonella enterica subsp. enterica serovar Typhimurium str. LT2
STM1161.S biofilm formation regulatory protein BssS from Salmonella typhimurium LT2
SC1109 putative cytoplasmic protein from Salmonella enterica subsp. enterica serovar Choleraesuis str. SC-B67
67% identity, 100% coverage

• In silico identification and experimental validation of PmrAB targets in Salmonella typhimurium by regulatory motif detection
  Marchal, Genome biology 2004
  • “...hit to putative outer membrane protein 0.764452 ATTAGTGTATACTTAAT m + 1111 All nine genomes? yceP STM1161 ; Ortholog of E. coli orf , hypothetical protein (AAC74144.1); Blast hit to putative cytoplasmic protein 0.764191 TTTATTGTTCATATAAT m + 1100 All nine genomes STM4098 putative arylsulfate sulfotransferase 0.763003 TCTAATATTTATTTAAT...”
• Media ion composition controls regulatory and virulence response of Salmonella in spaceflight
  Wilson, PloS one 2008
  • “...** small RNA STM0007 1.91 talB transaldolase B STM0389 1.85 x yaiA putative cytoplasmic protein STM1161.S 2.64 yceP putative cytoplasmic protein STM1369 2.81 x sufA putative HesB-like domain STM1371 2.65 x sufC putative ABC superfamily (atp_bind) transport protein STM1374 1.84 x ynhA putative SufE protein probably...”
• The addition of lac+ chromosome fragments to the E. coli proA-proB-lac deletion 13 chromosome
  Stodolsky, Genetics 1972
  • “...SC8301 sc1000 sc1002 sc1004 sc1100 SC1102 SC1108 sc1109 SClllO F' FHfH FFHfrH HfrH HfrH HfrH FFFFFFFFF- Relevant characters' prototroph lacIZYA deletion...”
  • “...ZacVl) rec+. The unstable structure is still present in SC1108, since its SC1109 ( A l l l / l a c V I ) rec+ derivative is Lac". Thus RecAf function is...”

EAE_16280 biofilm formation regulator BssS from Klebsiella aerogenes KCTC 2190
64% identity, 100% coverage

• Transcriptional effects of melatonin on the gut commensal bacterium Klebsiella aerogenes
  Graniczkowska, Genomics 2022
  • “...connector protein exponential 3.148 EAE_14345 AriR regulator of acid resistance influenced by indole exponential 3.088 EAE_16280 BssS biofilm formation regulatory protein exponential 1.675 EAE_14770 BssR regulator of biofilm through signal secretion exponential 1.819 Table 5 Relative expression of PTS genes in K. aerogenes grown with 1...”

YceP / b1060 regulator of biofilm formation from Escherichia coli K-12 substr. MG1655 (see 7 papers)
BSSS_ECOLI / P0AB33 Biofilm regulator BssS from Escherichia coli (strain K12) (see 2 papers)
c1327 biofilm formation regulatory protein BssS from Escherichia coli CFT073
NP_415578 regulator of biofilm formation from Escherichia coli str. K-12 substr. MG1655
b1060 orf, hypothetical protein from Escherichia coli str. K-12 substr. MG1655
64% identity, 100% coverage

• function: Represses biofilm formation in M9C glu and LB glu media but not in M9C and LB media. Seems to act as a global regulator of several genes involved in catabolite repression and stress response and regulation of the uptake and export of signaling pathways. Could be involved the regulation of indole as well as uptake and export of AI-2 through a cAMP-dependent pathway.
  disruption phenotype: Cells show increased biofilm formation when glucose is present in the medium. In a continuous-flow system with M9C medium supplemented with glucose, the biofilm had a 240-fold greater biomass, a 2800 fold-greater average thickness and a 16-fold increased surface coverage than the wild-type.
• 21st Congress of the European Hematology Association Copenhagen, Denmark, June 9–12, 2016
  , Haematologica 2016
• 46th Annual Meeting February 23-27, 2002, Moscone Convention Center, San Francisco, California : Wednesday, February 27, 2002, Part 3
  , Biophysical journal 2002
• YliH (BssR) and YceP (BssS) regulate Escherichia coli K-12 biofilm formation by influencing cell signaling.
  Domka, Applied and environmental microbiology 2006
  • GeneRIF: YceP (BssS) regulates biofilm formation through signal secretion together with YliH [BssS]
• Escherichia coli toxin/antitoxin pair MqsR/MqsA regulate toxin CspD
  Kim, Environmental microbiology 2010
  • “...repressor bssR b0836 3.3 1.3 1.2 Repressor of biofilm formation by indole transport regulation bssS b1060 1.2 3.0 2.5 Repressor of biofilm formation by indole transport regulation; global regulator, e.g. of AI-2 transport and motility genes mqsA b3021 3.5 3.7 2.5 Antitoxin part in MqsR-MqsA TA...”
• Sxy induces a CRP-S regulon in Escherichia coli
  Sinha, Journal of bacteriology 2009
  • “...E. COLI 5185 TABLE 1--Continued Gene Designation Induction (fold) b1060 b1322 b2592 b2614 b0014 b2699 b0966 b3686 b3687 b3635 b4140 b0631 bssS ycjF clpB grpE...”
• YcfR (BhsA) influences Escherichia coli biofilm formation through stress response and surface hydrophobicity
  Zhang, Journal of bacteriology 2007
  • “...b3512 b3506 b0019 b3509 b3510 b3511 b4376 b1283 b1060 b3494 b0014 b1646 b0814 b0966 Glutamate decarboxylase A subunit, acid resistance protein Glutamate...”
• YliH (BssR) and YceP (BssS) regulate Escherichia coli K-12 biofilm formation by influencing cell signaling
  Domka, Applied and environmental microbiology 2006
  • “...Here, it is shown that deletion of yceP (b1060) and yliH (b0836) increases biofilm formation in continuous-flow chambers with minimal glucose medium by...”
• Gene expression in Escherichia coli biofilms
  Ren, Applied microbiology and biotechnology 2004 (PubMed)
  • “...genes of unknown function (ybaJ, ychM, yefM, ygfA, b1060, b1112, b2377, b3022, b1373, b1601, and b0836). The DNA microarray results were corroborated with RNA...”
  • “...Anthranilate synthase component I 37 21 17 8 35 4 7 8 b1601 ygfA b1060 b1373 b0836 ychM yefM 5 5 4 3 3 2 2 6 8 5 1.3 3 3 3 b1601 b2912 b1060 b1373 b0836 b1206...”
• Global RNA half-life analysis in Escherichia coli reveals positional patterns of transcript degradation
  Selinger, Genome research 2003
  • “...b0553 b2398 b3494 b3556 b3685 b0726 b1205 b3362 b0162 b1060 b2080 b2377 b3361 b4132 b4396 yjfN IldD cpxP(2) cspG cpxP(1) nmpC yfeC uspB cspA yidE sucA ychH...”
• Combined, functional genomic-biochemical approach to intermediary metabolism: interaction of acivicin, a glutamine amidotransferase inhibitor, with Escherichia coli K-12
  Smulski, Journal of bacteriology 2001
  • “...b0806 b0836 b0865 b0897 b0964 b0966 b1003 b1045 b1050 b1060 b1103 b1104 b1105 b1107 b1108 b1111 b1112 b1128 b1145 b1168 b1178 b1195 b1205 b1256 b1257 b1273...”
• DNA microarray-mediated transcriptional profiling of the Escherichia coli response to hydrogen peroxide
  Zheng, Journal of bacteriology 2001
  • “...b4326 b2414 b4322 b2365 b4217 b2616 b4062 b2366 b3924 b1166 b2012 b2654 b0389 b1060 b3049 b1426 b3707 30 29 25 23 22 20 20 19 18 18 17 17 17 16 16 15 15 15 phoH...”
• More

B2G73_RS09175 biofilm formation regulator BssS from Citrobacter werkmanii
64% identity, 100% coverage

• Expression of a Shiga-Like Toxin during Plastic Colonization by Two Multidrug-Resistant Bacteria, Aeromonas hydrophila RIT668 and Citrobacter freundii RIT669, Isolated from Endangered Turtles (Clemmys guttata)
  Thomas, Microorganisms 2020
  • “...protein TAATGGGTTACAGCGAATAG 53.1 ATAAGACCACATAATAATCAGC 50.6 B2G73_RS10300 bssR biofilm formation regulatory protein CGCTTATCTGCTGTTGAG 52.9 ATACCGTGAAGTTGTGATTG 53.5 B2G73_RS09175 bssS biofilm formation regulatory protein GGACTGAAGTTGGACAAA 51.5 CGCTGATACTCATTTACCT 50.3 B2G73_RS19460 hmsP biofilm formation regulator GTTAATACTCACGGTAGC 45.1 GGTAATGCCAGTTGATAG 48.5 B2G73_RS15490 tabA Toxin-antitoxin biofilm protein GTCGGCAATATTCACAAC 52.0 TCATATCTTCGGCAATCA 53.3 B2G73_RS09280 csgD transcriptional...”

BHW77_11525 biofilm formation regulator BssS from Escherichia coli
ECs_1438 biofilm regulator from Escherichia coli O157:H7 str. Sakai
ECs1438 biofilm formation regulatory protein BssS from Escherichia coli O157:H7 str. Sakai
S1144 biofilm formation regulatory protein BssS from Shigella flexneri 2a str. 2457T
Z1697 orf, hypothetical protein from Escherichia coli O157:H7 EDL933
64% identity, 100% coverage

• Genomewide transcriptional response of Escherichia coli O157:H7 to norepinephrine
  Sharma, BMC genomics 2022
  • “...cyclase +2.87 3.86E-08 BHW77_21465 bolA transcriptional regulator +3.22 2.57E-05 BHW77_19190 bssR transcriptional regulator +2.76 1.25E-04 BHW77_11525 bssS transcriptional regulator +7.75 4.94E-08 BHW77_17570 flhC transcriptional regulator 1.62 2.44E-02 BHW77_16255 sodC superoxide dismutase + 2.81 3.37E-04 a Gene group/gene designations were selected from RAST Server [ 109 ]...”
• Pre-Harvest Survival and Post-Harvest Chlorine Tolerance of Enterohemorrhagic Escherichia coli on Lettuce
  Tyagi, Toxins 2019
  • “...1.7 ECs_1154 cbpM chaperone modulatory protein CbpM 1.8 1.8 ECs_1387 ybdM transcriptional regulator 2.1 1.7 ECs_1438 bssS transcriptional regulator biofilm 2.5 1.6 ECs_1683 ycgB SpoVR family stationary phase protein 1.7 1.6 ECs_1883 pspC envelope stress response membrane protein PspC 4.0 2.5 ECs_1885 pspE thiosulfate sulfurtransferase PspE...”
• Pre-Harvest Survival and Post-Harvest Chlorine Tolerance of Enterohemorrhagic Escherichia coli on Lettuce
  Tyagi, Toxins 2019
  • “...2.1 ECs1388 pchD Putative transcriptional regulator 3.7 3.9 ECs1417 csgD Transcriptional regulator CsgD 4.5 3.3 ECs1438 bssS biofilm regulator 3.4 4.2 ECs1490 bhsA multiple stress resistance protein (YcfR) 3.5 4.2 ECs1926 zntB Zinc transport protein ZntB 1.8 1.8 ECs2062 ybfL type IV secretion protein Rhs 3.9...”
• Gene expression induced in Escherichia coli O157:H7 upon exposure to model apple juice
  Bergholz, Applied and environmental microbiology 2009
  • “...ECs1243 ECs1246 ECs1293 ECs1318 ECs1342 ECs1350 ECs1397 ECs1438 ECs1441 ECs1488 ECs1490 ECs1576 ECs1588 ECs1593 ECs1612 ECs1654 ECs1655 ECs1691 ECs1760 ECs1763...”
• Global transcriptional response of Escherichia coli O157:H7 to growth transitions in glucose minimal medium
  Bergholz, BMC microbiology 2007
  • “...terE -2.90 1 ECs0507 ybaY 3.19 2 ECs1423 - 2.34 2 ECs0509 ybaA 2.56 2 ECs1438 yceP 4.78 2 ECs0518 aefA 2.12 2 ECs1466 yceD -2.86 1 ECs1467 rpmF -2.36 1 ECs2307 ydgG -2.69 1 ECs1500 potC -2.14 1 ECs2308 pntB -2.80 1 ECs1603 purB -3.58...”
• Addendum
  , Open forum infectious diseases 2019
• Comparison of strand-specific transcriptomes of enterohemorrhagic Escherichia coli O157:H7 EDL933 (EHEC) under eleven different environmental conditions including radish sprouts and cattle feces
  Landstorfer, BMC genomics 2014
  • “...(168) 3.3 (472) 0.5 (18) 0.5 (11) 3.8 (440) 0.3 (23) 5.6 (1336) 7.5 (0) Z1697 biofilm formation regulatory protein BssS 1 (113) 2.4 (386) 2.5 (116) 6.7 (10874) 4.4 (2326) 1.5 (89) 3.7 (512) 1.5 (219) 3.0 (556) 6.1 (4555) 4.7 (530) Z2243 nitrite extrusion...”
  • “...5 ). An additional indicator for adhesion to radish sprouts is the up-regulation of bssS (Z1697, Table 5 ), a regulatory gene for biofilm formation [ 92 ]. The increased transcription level of curli-related genes together with bssS corroborates the hypothesis of Fink et al ....”
• Transcriptional responses of Escherichia coli K-12 and O157:H7 associated with lettuce leaves
  Fink, Applied and environmental microbiology 2012
  • “...Symbol Description Day 1 Day 3 Biofilm Z1027 Z1697 ybiM yceP (bssS) Hypothetical protein Hypothetical protein 31.30 7.90 68.30 7.90 Cell envelope Z2775 Z1037...”

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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.