PaperBLAST

PaperBLAST Hits for RR42_RS31495 (75 a.a., MTILVRLDVL...)

Show query sequence

>RR42_RS31495
MTILVRLDVLLAERKMKSRELAQYIGITEPNLSLLKSGKVKGIRFDTLEKICEALNCQPG
DLLEYRADTPGEDQA

Running BLASTp...

Found 12 similar proteins in the literature:

PA5403 probable transcriptional regulator from Pseudomonas aeruginosa PAO1
Q9HTG1 Probable transcriptional regulator from Pseudomonas aeruginosa (strain ATCC 15692 / DSM 22644 / CIP 104116 / JCM 14847 / LMG 12228 / 1C / PRS 101 / PAO1)
73% identity, 88% coverage

• An atlas of the binding specificities of transcription factors in Pseudomonas aeruginosa directs prediction of novel regulators in virulence
  Wang, eLife 2021
  • “...the negative control for AlgB. ( C ) EMSA validation (monomer) for predicted binding of PA5403 in five promoters (PA5402, PA2439, PA4070, PA2784, and oprQ ). By contrast, the promoter fragment of pslA is used as the negative control for PA5403. ( D ) EMSA validation...”
  • “...By contrast, the promoter fragments of negative control DNA showing no binding to PA4984, AlgB, PA5403, AmgR, KdpE, and BqsR, respectively. The TF motifs are shown in the upper panel of EMSA, respectively. Arrows indicate half-sites in dimeric binding. Figure 2figure supplement 2. Validation of different...”
• The Small RNAs PA2952.1 and PrrH as Regulators of Virulence, Motility, and Iron Metabolism in Pseudomonas aeruginosa
  Coleman, Applied and environmental microbiology 2021 (secret)
• Nucleoid-associated proteins shape chromatin structure and transcriptional regulation across the bacterial kingdom
  Amemiya, Transcription 2021 (secret)
• Dissection of the cis-2-decenoic acid signaling network in Pseudomonas aeruginosa using microarray technique
  Rahmani-Badi, Frontiers in microbiology 2015
  • “...moaA1A2C, thiDl Transcription regulators rpoD, rpoN, PA0436, PA0512-PA0513, PA0515, PA1201,PA1399, PA1630, PA1859, PA2273, PA2432, PA2885, PA5403 EPS and LPS synthesis and secretion algABCDEFGIJLQRUWXZ, alg8, alg44, kdsA, pelABD, ddlA, pslB, mucBCD, wzt, waaACFG, rfaDE, wbpMWZ, wapR , lpxDO2, rmd, rmlC, PA1390, PA3242, PA3256, PA5238, PA5291 Aerobic and...”
• Gene expression in Pseudomonas aeruginosa swarming motility
  Tremblay, BMC genomics 2010
  • “...vs. non-swarming fold change (log 2 ) Transcriptional regulators PA0961 2 probable cold-shock protein 1.5 PA5403 1 probable transcriptional regulator 1.9 PA5550 glmR GlmR transcriptional regulator 1.6 Energy metabolism PA1552 ccoP1 probable cytochrome c 1.9 PA1553 ccoO1 probable cytochrome c oxidase subunit 2.1 PA1554 ccoN1 probable...”
  • “...lecA to be down-regulated under these conditions, to allow cells to freely migrate. Apart from PA5403 and PA5550 ( glmR / glpR ) (Table 2 ), nearly all genes belonging to the transcription factors class were down-regulated in tendril tip populations (Table 3 ), including a...”
• A Novel extracytoplasmic function (ECF) sigma factor regulates virulence in Pseudomonas aeruginosa
  Llamas, PLoS pathogens 2009
  • “...(PA2349 and PA5405), a homologue to the Fur regulator (PA2384), and a putative transcriptional regulator (PA5403). 10.1371/journal.ppat.1000572.g002 Figure 2 Genetic organization of the PUMA3 CSS system (black arrows) and part of the VreI (PA0675) regulon (grey arrows). Induction was determined by microarray analysis ( Table 1...”
  • “...membrane protein 2.5 PA4192 Probable ATP-binding component of polar amino acid ABC transport system 9.7 PA5403 Probable transcriptional regulator 10.3 PA5405 HUU; Putative lipoprotein export signal (predicted by LipoP) 5.8 a PA number attributed in the P. aeruginosa genome annotation project ( http://www.pseudomonas.com ) [52] ....”
• Proteome-wide identification of druggable targets and inhibitors for multidrug-resistant <i>Pseudomonas aeruginosa</i> using an integrative subtractive proteomics and virtual screening approach
  Vemula, Heliyon 2025

BPSL1564 putative transcriptional regulatory protein from Burkholderia pseudomallei K96243
66% identity, 97% coverage

• Predicting toxins found in toxin-antitoxin systems with a role in host-induced Burkholderia pseudomallei persistence
  Ross, Scientific reports 2020
  • “...when compared the published results, we only had an overlap of 8 toxins (BPSL0549A, BPSL0562, BPSL1564, BPSL2333, BPSS0390, BPSS0845a, BPSS2142, and BPSS1226), which may be due to the stringent size and gene structure filters used by the RASTA analysis (Supplemental Figure S3 A and B) 28...”
• Perturbation of the two-component signal transduction system, BprRS, results in attenuated virulence and motility defects in Burkholderia pseudomallei
  Lazar, BMC genomics 2016
  • “...1.09 1.34E-03 0.77 8.20E-03 BPSL1563 putative membrane protein of unknown function 1.22 5.17E-04 1.68 4.16E-05 BPSL1564 putative transcriptional regulatory protein 0.50 1.17E-01 1.37 9.39E-04 BPSL1598 putative transport-related, membrane protein 0.28 3.17E-01 1.59 1.66E-04 BPSL1829 putative methyl-accepting chemotaxis protein 1.98 4.26E-03 1.34# 1.89E-02 BPSL1872 putative N-acetylmuramoyl-L-alanine amidase...”
  • “...regulators Domain-input Domain-output BPSL0812 bpeR TetR family regulatory protein Increased Increased Not known TetR_N-DNA binding BPSL1564 transcriptional regulatory protein NS Increased Not known HTH_26-DNA binding BPSL2972 IclR family regulatory protein Decreased NS IclR/Small-molecule binding HTH_IclR-DNA binding BPSL3291 fliA flagellar biosynthesis sigma factor Increased Increased Not known...”

CC3270 transcriptional regulator, Cro/CI family from Caulobacter crescentus CB15
64% identity, 99% coverage

• Transcriptomic analysis of the stationary phase response regulator SpdR in Caulobacter crescentus
  da, BMC microbiology 2016
  • “...family transcriptional regulator CC3205 0.456 Transcription antitermination protein NusG CC3268 0.455 Protein of unknown function CC3270 0.394 Cro/CI family transcriptional regulator Upregulated CC2114 2.331 Methyltransferase of unknown specificity CC2234 2.924 Protein of unknown function CC3404 2.740 Protein of unknown function CC3654 29.412 Protein of unknown function...”
  • “...roles in modulating gene expression. Among the regulatory genes, there are three (CC0445, CC3164 and CC3270) predicted to encode transcriptional regulators, two belonging to the GntR family, whose members act on diverse biological processes, and one to the Cro/CI family [ 35 ]. Most if not...”

BTH_RS23845 helix-turn-helix domain-containing protein from Burkholderia thailandensis E264
64% identity, 97% coverage

• A Two-Component-System-Governed Regulon That Includes a β-Lactamase Gene is Responsive to Cell Envelope Disturbance
  Lee, mBio 2022
  • “...by one of the following regulators encoded by the genes included in the BesRS regulon: BTH_RS23845, BTH_RS07425, BTH_RS07880, BTH_RS09195, and BTH_RS08885 ( Fig.5A ). Among the operons, those putatively encoding the hopanoid biosynthesis, a macrolide efflux transporter, and the homoprotocatechuate degradation pathway, which we call the...”

SGGBAA2069_c18600 helix-turn-helix domain-containing protein from Streptococcus gallolyticus subsp. gallolyticus ATCC BAA-2069
61% identity, 88% coverage

• Transcriptome analysis of Streptococcus gallolyticus subsp. gallolyticus in interaction with THP-1 macrophage-like cells
  Grimm, PloS one 2017
  • “...system galactitol-specific transporter subunit IIB 1.18 n. r. 0.01 - 2.27 n. r. transcriptional regulator SGGBAA2069_c18600 putative transcriptional regulator 1.53 1.2 0.03 0.05 2.89 2.30 SGGBAA2069_c7250 LacI family transcriptional regulator n. r. 1.52 - 0.02 n. r. 2.87 SGGBAA2069_c10720 transcriptional regulator 1.03 n. r. 0.03 -...”

SSUSC84_0275 putative DNA-binding protein from Streptococcus suis SC84
62% identity, 84% coverage

• Screening of Virulence-Related Transcriptional Regulators in Streptococcus suis
  Liu, Genes 2020
  • “..., SSUSC84_1526 , SSUSC84_1572 , SSUSC84_1876 , and SSUSC84_1927 and for sxvR , SSUSC84_0029 , SSUSC84_0275 , SSUSC84_0648 , SSUSC84_0900 , SSUSC84_1526 , SSUSC84_1572 , SSUSC84_ 1782 and SSUSC84_1785 were selected. The primers ( Table S2 ) were designed according to the genomic sequence of S.suis...”
  • “...(to detect the SSUSC84_0111 gene), 0170-1/0170-2 (to detect the SSUSC84_0170 gene), 0275-1/0275-2 (to detect the SSUSC84_0275 gene), 0315-1/0315-2 (to detect the SSUSC84_0315 gene), 0756-1/0756-2 (to detect the SSUSC84_0756 gene), 1645-1/1645-2 (to detect the SSUSC84_1645 gene). (B) The capsules of WT, 0005 , 0111 , 0170 ,...”

cg1464 putative transcriptional regulatory protein from Corynebacterium glutamicum ATCC 13032
61% identity, 89% coverage

• Transcriptional regulation of the operon encoding stress-responsive ECF sigma factor SigH and its anti-sigma factor RshA, and control of its regulatory network in Corynebacterium glutamicum
  Busche, BMC genomics 2012
  • “...cg3077 Putative membrane protein 1.56 cg1410* rbsR Transcriptional repressor of ribose importer RbsACBD, LacI-family 1.54 cg1464 Putative transcriptional regulator, HTH_3-family 1.52 a Genes constituting a putative operon are indicated with the same symbol. The first gene in the operon is indicated with an asterisk. Underlined genes...”

FTN_0889 transcriptional regulator, cro/C1-type HTH domain from Francisella tularensis subsp. novicida U112
54% identity, 89% coverage

• The Drosophila melanogaster host model
  Igboin, Journal of oral microbiology 2012
  • “...Francisella novicida Adult (SI) FTN_0649 (FAD-dependent 4Fe-4S ferrodoxin) ( 268 ) * FTN_0869 (putative transglutaminase) FTN_0889 (putative transcriptional regulator) glpD (anaerobic glycerol-3-phosphate dehydrogenase) nadC (nicotinate-nucleotide pyrophosphorylase) OxyR (oxidative stress transcriptional regulator) pmrA response regulator udp (uridine phosphorylase) uvrA, uvrB, recB, ssb, mutM, ruvC (DNA repair) DNA...”
• Francisella-arthropod vector interaction and its role in patho-adaptation to infect mammals
  Akimana, Frontiers in microbiology 2011
  • “...(POT) family protein yhiP FTN_0886 Hypothetical membrane protein FTN_0887 Hypothetical protein FTN_0888 Hypothetical membrane protein FTN_0889 Helix-turn-helix family protein FTN_0891 Holliday junction DNA helicase, subunit B ruvB FTN_0898 Amino acid permease FTN_0900 Protein of unknown function with predicted hydrolase and phosphorylase activity FTN_0921 FKBP-type peptidyl-prolyl cis...”
• Reciprocal analysis of Francisella novicida infections of a Drosophila melanogaster model reveal host-pathogen conflicts mediated by reactive oxygen and imd-regulated innate immune response
  Moule, PLoS pathogens 2010
  • “...to Polymyxin B as measured by disk diffusion assay. Error bars represent standard error. pmrA, FTN_0889, udp, glpD and FTN_0649 are statistically significantly different from U112 with 2-tailed t-test P values of 0.0299, 0.0041, 0.0495, 0.0065 and 0.0447 respectively. FTN_0869 and nadC are not significantly different...”
  • “...flies ( Figure 4C ). These genes were the orphan response regulator pmrA, the gene FTN_0889 which is a helix-turn-helix protein and putative transcriptional regulator, glpD which is an anaerobic glycerol-3-phosphate dehydrogenase, the nicotinate-nucleotide pyrophosphorylase nadC, a uridine phosphorylase udp, FTN_0649, a FAD-dependent 4Fe-4S ferrodoxin, and...”

SAM23877_4016 helix-turn-helix domain-containing protein from Streptomyces ambofaciens ATCC 23877
51% identity, 97% coverage

• Synteruptor: mining genomic islands for non-classical specialized metabolite gene clusters
  Haas, NAR genomics and bioinformatics 2024
  • “...128 438 SAM23877_5592 - SAM23877_5660 spiramycin/NRP SMBGC GI-3 62 4 270 811 4 326 714 SAM23877_4016 - SAM23877_4077 pSAM2-xSAM1 GI-4 52 6 965 819 7 022 659 SAM23877_6462 - SAM23877_6513 contains CRISPR system GI-5 49 316 599 358 923 SAM23877_0359 - SAM23877_0407 unknown GI-6 45 7...”

CG479_RS12175 helix-turn-helix domain-containing protein from Bacillus cytotoxicus
59% identity, 84% coverage

• Whole-genome-based phylogeny of Bacillus cytotoxicus reveals different clades within the species and provides clues on ecology and evolution
  Stevens, Scientific reports 2019
  • “...CRISPR-associated protein Cas4 G479_RS11880 G479_RS11880 acyltransferase CG479_RS11890 CG479_RS11890 N-acetyltransferase CG479_012025 CG479_012025 phosphonate ABC transporter permease CG479_RS12175 CG479_RS12175 transcriptional regulator CG479_RS12350 CG479_RS12350 IS30 family transposase G479_RS12365 G479_RS12365 MATE family efflux transporter CG479_RS12655 CG479_RS12655 IS256 family transposase CG479_RS12690 CG479_RS12690 ArsR family transcriptional regulator CG479_RS12835 CG479_RS12835 enterotoxin G479_RS15125 G479_RS15125...”

LACR_0302 Predicted transcriptional regulator from Lactococcus lactis subsp. cremoris SK11
35% identity, 28% coverage

• Strain-Dependent Transcriptome Signatures for Robustness in Lactococcus lactis
  Dijkstra, PloS one 2016
  • “...site-specific tyrosine recombinase XerS positive 16.5 LACR_C54 hypothetical protein positive 4.8 LACR_0329 acetyltransferase positive 3.0 LACR_0302 transcriptional regulator positive 2.0 LACR_0398 asnB asparagine synthetase B negative 17.5 LACR_A05 hypothetical protein positive 3.0 LACR_2026 ABC-type oligopeptide transport system, periplasmic component negative 4.4 LACR_2220 hypothetical protein positive 1.4...”

FOA15_RS11890 helix-turn-helix domain-containing protein from Paenibacillus kribbensis
32% identity, 84% coverage

• Comparative Genomics Insights into a Novel Biocontrol Agent Paenibacillus peoriae Strain ZF390 against Bacterial Soft Rot
  Zhao, Biology 2022
  • “...B, pqq D 24,119 bp 13018621325980 Fungi, bacteria, virus IAQ67_05860- IAQ67_05975 ABE82_06065-ABE82_06175 PPSQR21_012140-PPSQR21_012370 C1A50_1276-C1A50_1299 FOA15_RS11780- FOA15_RS11890 Tridecaptin NRPS fus AA, bac C 92,515 bp 24193212511835 G - bacteria IAQ67_11205- IAQ67_11360 ABE82_11520-ABE82_11675 PPSQR21_022460-PPSQR21_022870 C1A50_2315-C1A50_2359 FOA15_RS17145- FOA15_RS17325 Unknown Siderophore sbn CEF 17,402 bp 999368 1016769 NA IAQ67_04460- IAQ67_04525...”

New Search

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.