PaperBLAST

PaperBLAST Hits for CCNA_02315 (64 a.a., MKNRLKVLRA...)

Show query sequence

>CCNA_02315
MKNRLKVLRAERDWSQADLADRLEVSRQTINALETGKYDPSLPLAFKIARLFGQPIESIF
QDEA

Running BLASTp...

Found 67 similar proteins in the literature:

CCNA_02315 transcriptional regulator, Cro/CI family from Caulobacter crescentus NA1000
100% identity, 100% coverage

• The type IV pilin PilA couples surface attachment and cell-cycle initiation in Caulobacter crescentus
  Del, Proceedings of the National Academy of Sciences of the United States of America 2020
  • “...under slow-growth conditions. Cluster C comprised the antisigma factor nepR , a Cro/CI transcription factor (CCNA_02315), and xseB encoding the small subunit of the exodeoxyribonuclease VII ( Fig. 1 D and SI Appendix , Fig. S3 ), which form outer-circle components not directly linked to c-di-GMP...”

PA4077 probable transcriptional regulator from Pseudomonas aeruginosa PAO1
PA14_11150 putative transcriptional regulator from Pseudomonas aeruginosa UCBPP-PA14
73% identity, 91% coverage

• MeSH ORA framework: R/Bioconductor packages to support MeSH over-representation analysis
  Tsuyuzaki, BMC bioinformatics 2015
  • “...PA3303 - 882468 (control) - - - PA0392 - 878514 Conserved hypothetical - - - PA4077 - 878707 Transcriptional regulator - - - PA5199 amgS 880300 Two-component sensor Phosphorelay signal transduction system Phosphorelay sensor kinase activity - PA5366 pstB 881628 Phosphate transport Transport - Membrane (+1)...”
  • “...p=0 PA3303 - - - - - - PA0392 - - - - - - PA4077 - - - - - - PA5199 Periplasm (+7) Bacillus subtilis (+9) Chromosome Deletion DNA, Bacteria (+88) Gene Knockout (+39) Alleles (+98) PA5366 Cell Membrane (+1) Escherichia coli (+5) Chromosome...”
• Genome-scale identification of resistance functions in Pseudomonas aeruginosa using Tn-seq
  Gallagher, mBio 2011
  • “...1.0 PA0392 Conserved hypothetical 644 (5) 1,374 (5) 0 (0) 0 No 2 f 0.25 PA4077 Transcriptional regulator 1,572 (3) 1,230 (3) 0 (0) 0 No 1 f 0.25 PA5199 amgS Two-component sensor 764 (18) 663 (20) 0 (0) 0 Yes 0.125 PA5366 pstB Phosphate transport...”
  • “...several new tobramycin resistance functions whose inactivation greatly increased sensitivity, including PA1805 ( ppiD ), PA4077, and PA0392 ( Table2 ). PA1805 encodes a peptidyl-prolyl cis - trans isomerase and is thought to facilitate the folding of membrane and exported proteins (1214). Since misfolded proteins resulting...”
• Uracil influences quorum sensing and biofilm formation in Pseudomonas aeruginosa and fluorouracil is an antagonist
  Ueda, Microbial biotechnology 2009
  • “...PA14_16010 PA3741 6.1 1.1 7.5 Hypothetical protein PA14_13660 PA3885 5.7 1.5 1.9 Hypothetical protein PA14_11150 PA4077 7.5 4.9 1.3 Probable transcriptional regulator PA14_09660 PA4198 16 1.1 13.9 Probable AMPbinding enzyme PA14_67190 PA5088 7.5 2 3 Hypothetical protein PA14_67860 PA5139 4.9 2.3 10.6 Hypothetical protein PA14_71890 PA5445...”
• Uracil influences quorum sensing and biofilm formation in Pseudomonas aeruginosa and fluorouracil is an antagonist
  Ueda, Microbial biotechnology 2009
  • “...dehydrogenase PA14_16010 PA3741 6.1 1.1 7.5 Hypothetical protein PA14_13660 PA3885 5.7 1.5 1.9 Hypothetical protein PA14_11150 PA4077 7.5 4.9 1.3 Probable transcriptional regulator PA14_09660 PA4198 16 1.1 13.9 Probable AMPbinding enzyme PA14_67190 PA5088 7.5 2 3 Hypothetical protein PA14_67860 PA5139 4.9 2.3 10.6 Hypothetical protein PA14_71890...”

MJ0272 repressor protein, putative (yorfE) from Methanocaldococcus jannaschii DSM 2661
65% identity, 76% coverage

• Genomic characterization of methanomicrobiales reveals three classes of methanogens
  Anderson, PloS one 2009
  • “...sigma factors [23] , and the Methanomicrobiales have homologs of three of these proteins (MJ0173, MJ0272, and MJ1243). However, the SpoIIAB anti-sigma factor binds to three separate regions of sigma F [24] corresponding to conserved regions 2, 3, and 4, and regions 2 and 3 are...”

TK1339 predicted transcription regulator, containing DNA-binding HTH domain from Thermococcus kodakaraensis KOD1
64% identity, 98% coverage

• The TK0271 Protein Activates Transcription of Aromatic Amino Acid Biosynthesis Genes in the Hyperthermophilic Archaeon Thermococcus kodakarensis
  Yamamoto, mBio 2019
  • “...that were expressed in these lanes were TK0063, TK0142, TK0169, TK0271, TK0888, TK1210, TK1227, TK1272, TK1339, TK1489, TK1881, TK1955, TK2190, and TK2229. We carried out the same experiments with other DNA probes and found that the TK0271 protein was the only protein that displayed specificity to...”

TEMA_35430 helix-turn-helix transcriptional regulator from Terrisporobacter mayombei
58% identity, 91% coverage

• Genome-based metabolic and phylogenomic analysis of three Terrisporobacter species
  Böer, PloS one 2023
  • “...Toxin Hemolysin Undetermined TEMA_35520 TEPE_06520 TEGL_05930 Undetermined TEMA_18780 TEPE_30320 TEGL_29320 Cytolysin ( Enterococcus ) cylR2 TEMA_35430 TEPE_25820 TEGL_05860 Antiphagocytosis Capsular polysaccharide ( Vibrio ) rmlB - TEPE_11780 - Capsule ( Enterococcus ) TEMA_02390 TEPE_14200 TEGL_14000 Cell surface components Trehalose-recycling ABC transporter ( Mycobacterium ) sugC TEMA_29560...”

HMPREF0421_21055 helix-turn-helix transcriptional regulator from Gardnerella vaginalis ATCC 14019
57% identity, 90% coverage

• Comparative genomics of Gardnerella vaginalis strains reveals substantial differences in metabolic and virulence potential
  Yeoman, PloS one 2010
  • “...608 HipB-family TA system antitoxin 98/100/98 HMPREF0424_0512 HMPREF0421_21057 609 PHD-family TA system antitoxin 99/100/99 HMPREF0424_0517 HMPREF0421_21055 610 HigA-family TA system antitoxin 99/100/99 HMPREF0424_0518 n/a n/a RelB-family TA system antitoxin -/-/- n/a HMPREF0421_21053 612 RelE-family TA system toxin -/100/- n/a HMPREF0421_21052 613 RelE-family TA system toxin -/100/-...”

GBAA_2523 helix-turn-helix transcriptional regulator from Bacillus anthracis str. 'Ames Ancestor'
57% identity, 91% coverage

• Divergence of the SigB regulon and pathogenesis of the Bacillus cereus sensu lato group
  Scott, BMC genomics 2012
  • “...GBAA_1939 Hypothetical protein bID_Cluster_5559 2 GBAA_2162 Hypothetical protein bID_Cluster_11158 3 GBAA_2384 Hypothetical protein bID_Cluster_13854 4 GBAA_2523 HTH DNA-binding protein bID_Cluster_618 5 GBAA_3291 Methyl-accepting chemotaxis protein bID_Cluster_3242 6 GBAA_3338 S-layer protein bID_Cluster_2077 7 GBAA_5674 Hypothetical protein Clade A 5 bID_Cluster_6809 1 BMB171_C1598 two-component response regulator, LuxR family...”

HMPREF0424_0517 DNA-binding protein from Gardnerella vaginalis 409-05
57% identity, 90% coverage

• Comparative genomics of Gardnerella vaginalis strains reveals substantial differences in metabolic and virulence potential
  Yeoman, PloS one 2010
  • “...HMPREF0421_21058 608 HipB-family TA system antitoxin 98/100/98 HMPREF0424_0512 HMPREF0421_21057 609 PHD-family TA system antitoxin 99/100/99 HMPREF0424_0517 HMPREF0421_21055 610 HigA-family TA system antitoxin 99/100/99 HMPREF0424_0518 n/a n/a RelB-family TA system antitoxin -/-/- n/a HMPREF0421_21053 612 RelE-family TA system toxin -/100/- n/a HMPREF0421_21052 613 RelE-family TA system toxin...”

BA0391 DNA-binding protein from Bacillus anthracis str. Ames
53% identity, 94% coverage

• Whole genome protein microarrays for serum profiling of immunodominant antigens of Bacillus anthracis
  Kempsell, Frontiers in microbiology 2015
  • “...to external environmental stimuli (Carlson et al., 2009 ). Some of these e.g., BA3828 and BA0391 are transcription factors which are differentially regulated between the two groups. The former is specific to the TCA group and the latter the AP IVDU group. These merit further follow...”

LMOf2365_0435 DNA-binding protein from Listeria monocytogenes str. 4b F2365
lmo0416 similar to putative transcription regulator from Listeria monocytogenes EGD-e
57% identity, 94% coverage

• Transcriptomic Analysis of Listeria monocytogenes in Response to Bile Under Aerobic and Anaerobic Conditions
  Chakravarty, Frontiers in microbiology 2021
  • “...2 domain protein 12.4 LMOf2365_2322 LysR family transcriptional regulator, regulator of the ytmI operon 13.1 LMOf2365_0435 DNA-binding protein 14.2 LMOf2365_2799 DNA-binding protein 14.7 Gene ID Gene product Transcript levels LMOf2365_1010 Transcriptional regulator, MarR family 18.4 LMOf2365_2233 Transcriptional regulator, MarR family 19.1 LMOf2365_0755 Transcriptional regulator, PadR family...”
• SecA2 Associates with Translating Ribosomes and Contributes to the Secretion of Potent IFN-β Inducing RNAs
  Teubner, International journal of molecular sciences 2022
  • “...acid transport and metabolism 0.12 0.15 lmo2620 rplE 50S ribosomal protein L5 Translation 0.12 0.15 lmo0416 Uncharacterized protein. DNA-binding. putative regulator Transcription 0.14 0.14 lmo1052 pdhA Pyruvate dehydrogenase (Acetyl-transferring) E1 component. alpha subunit Energy production and conversion 0.10 0.13 lmo2458 pgk Phosphoglycerate kinase Carbohydrate transport and...”
• PadR-type repressors controlling production of a non-canonical FtsW/RodA homologue and other trans-membrane proteins
  Hauf, Scientific reports 2019
  • “...lmo2050 excinuclease ABC subunit A 2.30.4 0.0037 downregulated in lstR lmo1597 hypothetical protein 0.50.04 0.0083 lmo0416 putative transcriptional regulator 0.50.01 0.0017 lmo0417 hypothetical protein 0.40.02 0.0084 lmo1839 PyrP similar to uracil permease 0.20.06 0.0074 upregulated in lltR * fold induction lltR */wt lmo0599 LltR, PadR-like transcriptional...”
  • “...read-through could be an explanation for this. The remaining LstR-affected genes, among which is the lmo0416 gene coding for a putative transcriptional regulator, show lower fold changes and it remains unclear whether these are direct or secondary effects. A similar hierarchy in fold changes was observed...”
• Listeria monocytogenes PerR mutants display a small-colony phenotype, increased sensitivity to hydrogen peroxide, and significantly reduced murine virulence
  Rea, Applied and environmental microbiology 2005
  • “...sequence were identified upstream of the start codons of lmo0416, lmo0106, lmo2146, and lmo2165. It is possible that in the absence of PerR one of these...”

PAP_06600 helix-turn-helix transcriptional regulator from Palaeococcus pacificus DY20341
58% identity, 98% coverage

• Metabolic Adaptation to Sulfur of Hyperthermophilic Palaeococcus pacificus DY20341^T from Deep-Sea Hydrothermal Sediments
  Zeng, International journal of molecular sciences 2020
  • “...barophilus MP) PAP_04120 52 364 2.80 1.53 10 62 Hypothetical protein ( Thermococcus barophilus MP) PAP_06600 10 70 2.80 2.49 10 13 Cro regulatory protein ( Thermococcus litoralis DSM 5473) ijms-21-00368-t002_Table 2 Table 2 The expression difference of key genes in S 0 -reduction system between...”

lmo2408 similar to repressor protein from Listeria monocytogenes EGD-e
48% identity, 96% coverage

• Listeria monocytogenes grown at 7° C shows reduced acid survival and an altered transcriptional response to acid shock compared to L. monocytogenes grown at 37° C
  Ivy, Applied and environmental microbiology 2012
  • “...murC, ndk lmo2210 lmo0998, lmo1597, lmmo1965 lmo952, lmo1749, lmo2408 lmo1049, atpI lmo2293 lmo0903 lmo1926 lmo0883 0 0 0 1 lmo1639 0 3 lmo0217, lmo1828,...”
  • “...lmo2260 lmo2261 lmo2293 lmo2295 lmo2296 lmo2362 lmo2363 lmo2408 lmo2409 lmo2484 lmo2487 lmo2625 (rplP) lmo2630 (rplW) lmo2632 (rplC) lmo2633 (rpsJ) 5 min...”
• Probing the pan-genome of Listeria monocytogenes: new insights into intraspecific niche expansion and genomic diversification
  Deng, BMC genomics 2010
  • “...BglG family IIIA + - lmo2144 Similar to transcription regulator, GntR family IIIA - - lmo2408 Similar to repressor protein IIIA + - lmo2732 Similar to transcription regulator, RpiR family IIIA - - lmo2773 Similar to transcription antiterminator IIIA + - lmo2851 Similar to transcription regulator,...”

BTF1_25170 helix-turn-helix transcriptional regulator from Bacillus thuringiensis HD-789
53% identity, 88% coverage

• NagR_Bt Is a Pleiotropic and Dual Transcriptional Regulator in Bacillus thuringiensis
  Cao, Frontiers in microbiology 2018
  • “...NT BTF1_24980 crr PTS system glucose-specific transporter subunit IIA 251 acttgtctagaggtct 8.87 75.026 23.846 1.973 BTF1_25170 XRE family transcriptional regulator / / / 33.600 NT BTF1_25685 lrgB Antiholin-like protein LrgB / / / 19.299 NT BTF1_25690 lrgA Murein hydrolase regulator LrgA / / / 10.165 NT...”

BLi04122 putative protein from Bacillus licheniformis DSM 13
51% identity, 66% coverage

• Identification of a novel two-peptide lantibiotic, lichenicidin, following rational genome mining for LanM proteins
  Begley, Applied and environmental microbiology 2009
  • “...211 5 TMS COG1131 BLi04121 (YP_093627) 95 BLi04122 (YP_093628) 92 BLi04123 (YP_093629) 62 BLi04124 (YP_093630) 443 BLi04125 (YP_093631) 718 BLi04126 (YP_093632)...”
  • “...encode the putative self-protection immunity genes lanEFG. BLi04122 encodes a putative regulator that shows significant homology (38% identity) to LtnR (GenBank...”
• Production of the novel two-peptide lantibiotic lichenicidin by Bacillus licheniformis DSM 13
  Dischinger, PloS one 2009
  • “...genome of B. halodurans C-125 (BH1491, 49%) [25] . BLi04123 is a small hypothetical protein. BLi04122 constitutes a helix-turn-helix protein that shows 60% similarity to a protein that is encoded near the haloduracin gene cluster (BH0460) and may be involved in regulation. BLi04121 is a small...”

2xiuA / Q8VL32 High resolution structure of mtsl-tagged cylr2. (see paper)
56% identity, 89% coverage

• Ligand: s-[(1-oxyl-2,2,5,5-tetramethyl-2,5-dihydro-1h-pyrrol-3-yl)methyl] methanesulfonothioate (2xiuA)

EF0524 transcriptional regulator, Cro/CI family from Enterococcus faecalis V583
56% identity, 89% coverage

• Whole-genome mapping of 5' RNA ends in bacteria by tagged sequencing: a comprehensive view in Enterococcus faecalis
  Innocenti, RNA (New York, N.Y.) 2015
  • “...the transcript that contains ef0522 ef0523 in an operon is antisense to a transcript carrying ef0524 . Similar examples are observed on plasmids pTEF1 and pTEF2 (the ppRNome browser and Supplemental Table SF). However, one of the most striking antisense organizations was found in the region...”

MUS_4114 helix-turn-helix transcriptional regulator from Bacillus velezensis YAU B9601-Y2
50% identity, 96% coverage

• Transcriptome Analysis of Bacillus amyloliquefaciens Reveals Fructose Addition Effects on Fengycin Synthesis
  Lu, Genes 2022
  • “...factors, such as HTH-type transcriptional regulator (alsR, ydhC2 , citR , yuxN , cueR , MUS_4114 , norG1 , yazB1 ), DeoR family transcriptional regulator ( fruR ), response regulator ( ComA ), the expression of 23 transcriptional regulatory factors, including polymerase sporulation-specific sigma factor (...”

RBAM_034550 putative transcriptional regulator from Bacillus amyloliquefaciens FZB42
50% identity, 96% coverage

• Depressed biofilm production in Bacillus amyloliquefaciens C06 causes γ-polyglutamic acid (γ-PGA) overproduction
  Liu, Current microbiology 2011 (PubMed)
  • “...associated with an ORF showing high similarity to RBAM_034550 from B. amyloliquefaciens FZB42. In this paper, the ORF was designated pbrA, standing for c-PGA...”
  • “...the disrupted gene in M306 had high similarity to RBAM_034550 from B. amyloliquefaciens FZB42, and this gene was designated pbrA, which 123 J. Liu et al.:...”

MSMEG_5542 transcriptional regulator, HTH_3 family protein from Mycobacterium smegmatis str. MC2 155
50% identity, 69% coverage

• MnoSR removal in Mycobacterium smegmatis triggers broad transcriptional response to 1,3-propanediol and glucose as sole carbon sources
  Płocińska, Frontiers in cellular and infection microbiology 2024
  • “...factor RsbW (MSMEG_1803) was upregulated by more than 28-fold. Another potential target for SigF-dependent regulation, MSMEG_5542 (an HTH3 family transcription factor), was also among the most strongly upregulated genes, with its expression during carbon starvation reaching more than 97-fold of the level recorded under carbon-rich conditions....”
• Characterization of Mycobacterium smegmatis sigF mutant and its regulon: overexpression of SigF antagonist (MSMEG_1803) in M. smegmatis mimics sigF mutant phenotype, loss of pigmentation, and sensitivity to oxidative stress
  Singh, MicrobiologyOpen 2015
  • “...channel 3.78/3.41 GTCTN 16 GGGGA 80 MSMEG_5540 Conserved hypothetical protein 2.59/2.34 GTTTN 17 GGGTA 792 MSMEG_5542 Transcriptional regulator, HTH_3 family 4.82/4.69 GTTTN 17 GGGTA 518 MSMEG_5543 a Hypothetical protein 5.13/5.91 GTTTN 17 GGGTA 77 MSMEG_5590 Carboxylateamine ligase 5.48/3.09 GTTTN 15 GGGCA 14 MSMEG_5605 Cytochrome bd ubiquinol...”
  • “...In this study, using our selection criteria (2fold, P 0.05), we identified three transcriptional regulators; MSMEG_5542 (HTH3 family), MSMEG_5731 (GntR family), and MSMEG_6508 (MarR family) which showed reduced expression in exponential phase, and MSMEG_5542, MSMEG_5301 (TetR family) with reduced expression in stationary phase. Of these MSMEG_5542,...”
• Gene Expression, Bacteria Viability and Survivability Following Spray Drying of Mycobacterium smegmatis
  Lauten, Materials (Basel, Switzerland) 2010
  • “...conserved hypothetical protein 0.9 9.1 0.018 89% MSMEG_5343 conserved hypothetical protein 1.1 9.2 0.010 98% MSMEG_5542 transcriptional regulator, HTH_3 family protein 1.0 9.4 0.008 93% MSMEG_5543 hypothetical protein 1.8 10.4 0.002 99% MSMEG_5616 glyoxalase/bleomycin resistance protein/dioxygenase 0.7 8.7 0.017 89% MSMEG_5617 immunogenic protein MPT63 1.6 10.6...”
  • “...12.2 25% MSMEG_4208 integral membrane protein -0.9 10.8 60% MSMEG_5152 hypothetical protein -0.8 11.9 27% MSMEG_5542 transcriptional regulator, HTH_3 family protein 1.4 10.1 55% MSMEG_6213 Manganese containing catalase 1.0 10.3 55% MSMEG_6242 alcohol dehydrogenase, iron-containing -1.3 12.4 51% MSMEG_6579 conserved hypothetical protein 1.1 11.5 21% MSMEG_6759...”
• The SigF regulon in Mycobacterium smegmatis reveals roles in adaptation to stationary phase, heat, and oxidative stress
  Hümpel, Journal of bacteriology 2010
  • “...MSMEG_4562 MSMEG_4993 MSMEG_5342 MSMEG_5343 MSMEG_5400 MSMEG_5542 MSMEG_5590 MSMEG_5606 MSMEG_5616 MSMEG_5721 MSMEG_5826 MSMEG_5936 MSMEG_6210 MSMEG_6213...”

SAG0169 transcriptional regulator, Cro/CI family from Streptococcus agalactiae 2603V/R
58% identity, 88% coverage

• Adaptive response of neonatal sepsis-derived Group B Streptococcus to bilirubin
  Hansen, Scientific reports 2018
  • “...transporter subunit IIA 1.34 4.07E-05 1.29E-02 SAG1899 PTS system transporter subunit IIC 1.83 5.82E-05 1.59E-02 SAG0169 Formate acetyltransferase 1.32 1.26E-04 2.46E-02 SAG1350 Surface antigen-like protein 2.02 1.28E-04 2.46E-02 SAG0680 Hypothetical protein 0.41 1.29E-04 2.46E-02 SAG0325 Pyruvate formate-lyase-activating enzyme 1.81 1.91E-04 3.31E-02 SAG1900 PTS system transporter subunit...”
• Genetic islands of Streptococcus agalactiae strains NEM316 and 2603VR and their presence in other Group B streptococcal strains
  Herbert, BMC microbiology 2005
  • “...sag2063 clp proteases sag1294 and sag1585 Transporters sag1517, sag1998-90, sag1902 and sag1934 Regulators sag0048, sag0124, sag0169, sag 0637, sag0644, sag1128, sag1332, sag1359, sag1409 ( rogB ), sag1463 (encoding a RALP) , sag1791, and sag1956-7 ( rgf ) Encoding other proteins sag0031, sag 0624, sag0662 ( cyl...”

AF1627 repressor protein from Archaeoglobus fulgidus DSM 4304
WP_010879124 helix-turn-helix transcriptional regulator from Archaeoglobus fulgidus DSM 4304
53% identity, 85% coverage

• Transcription in archaea
  Kyrpides, Proceedings of the National Academy of Sciences of the United States of America 1999
  • “...AF2127 AF1022 AF2232 AF0673 AF1270 AF1298 AF1697 AF2136 AF1627 AF1793 AF2425 AF0439 AF0474 AF0584 AF1121 AF1148 AF1404 AF1448 AF1622 AF1723 AF1743 A. fulgidus...”
• Comparative genomics of DNA-binding transcription factors in archaeal and bacterial organisms
  Martinez-Liu, PloS one 2021
  • “...of Methanothermobacter defluvii or global regulators such as the h-t-h transcriptional regulator of Archaeoglobus fulgidus (WP_010879124). In this regard, the cell surface proteins that mediate bacterial attachment, cell surface carbohydrates and proteins that protect the bacterial cell, in addition to hydrolytic enzymes may contribute to the...”

TEGL_05860 helix-turn-helix transcriptional regulator from Terrisporobacter glycolicus ATCC 14880 = DSM 1288
57% identity, 80% coverage

• Genome-based metabolic and phylogenomic analysis of three Terrisporobacter species
  Böer, PloS one 2023
  • “...Undetermined TEMA_35520 TEPE_06520 TEGL_05930 Undetermined TEMA_18780 TEPE_30320 TEGL_29320 Cytolysin ( Enterococcus ) cylR2 TEMA_35430 TEPE_25820 TEGL_05860 Antiphagocytosis Capsular polysaccharide ( Vibrio ) rmlB - TEPE_11780 - Capsule ( Enterococcus ) TEMA_02390 TEPE_14200 TEGL_14000 Cell surface components Trehalose-recycling ABC transporter ( Mycobacterium ) sugC TEMA_29560 TEPE_00240 TEGL_00240...”

GALLO_RS00675 helix-turn-helix transcriptional regulator from Streptococcus gallolyticus UCN34
52% identity, 91% coverage

• Genome-Based Drug Target Identification in Human Pathogen Streptococcus gallolyticus
  Qureshi, Frontiers in genetics 2021
  • “...protein DnaA GALLO_RS00200 DEG10200056 80.769 Glucan-binding protein C GALLO_RS00610 DEG10010101 54.688 Membrane protein insertase YidC GALLO_RS00675 DEG10380051 53.659 Transcriptional regulator CtsR SGGBAA2069_ RS00890 DEG10280041 51.448 PTS fructose transporter subunit IIA GALLO_RS00830 DEG10470198 50 Penicillin-binding protein 2A SGGBAA2069_ RS01250 DEG10180105 47.283 AraC family transcriptional regulator GALLO_RS01215 DEG10110082...”

MOV58_01130 helix-turn-helix transcriptional regulator from Staphylococcus hominis
48% identity, 90% coverage

• The Ubiquitous Human Skin Commensal Staphylococcus hominis Protects against Opportunistic Pathogens
  Severn, mBio 2022
  • “...genes were colocalized on the S. hominis AH5009 genome, ranging from locus tag MOV58_01105 to MOV58_01130. While the specific function of these genes is unclear given the few prior functional studies in any S. hominis strain, MOV58_01110 was predicted by BLASTx to be an arylamine N...”

BH0460 transcriptional regulator from Bacillus halodurans C-125
49% identity, 82% coverage

• Production of the novel two-peptide lantibiotic lichenicidin by Bacillus licheniformis DSM 13
  Dischinger, PloS one 2009
  • “...that shows 60% similarity to a protein that is encoded near the haloduracin gene cluster (BH0460) and may be involved in regulation. BLi04121 is a small protein that also is similar (61%) to a protein encoded downstream of the haloduracin gene cluster (BH0459) [25] and harbors...”

SP_2119 transcriptional regulator, putative from Streptococcus pneumoniae TIGR4
49% identity, 89% coverage

• Multi-omic profiling to assess the effect of iron starvation in Streptococcus pneumoniae TIGR4
  Jiménez-Munguía, PeerJ 2018
  • “...Downregulated 38898 SP_2085, SP_2086, SP_2087, SP_2088 4/4 Downregulated 38906 SP_2115, SP_2117 2/3 Downregulated 38907 SP_2118, SP_2119 2/3 Downregulated 38929 SP_2235, SP_2236 2/3 Downregulated The differentially expressed genes were annotated with Gene Ontology terms, using Blast2GO ( Fig. 2 ). According to the molecular function level, the...”

SPD_1947 transcriptional regulator, putative from Streptococcus pneumoniae D39
49% identity, 93% coverage

• Klebsiella pneumoniae peptide hijacks a Streptococcus pneumoniae permease to subvert pneumococcal growth and colonization
  Lux, Communications biology 2024
  • “...strain D39 after 15min of exposure to 0.5mg/ml peptide V11A Protein Gene Description off A0A0H2ZMI0 SPD_1947 Transcriptional regulator, putative A0A0H2ZNK9 SPD_1651 Iron-compound ABC transporter, ATP-binding protein A0A0H2ZNQ1 rimI [Ribosomal protein S18]-alanine N-acetyltransferase A0A0H2ZP12 cbpD Choline binding protein D A0A0H2ZPD7 SPD_0908 Sua5/YciO/YrdC/YwlC family protein A0A0H2ZQ49 SPD_0072 Glyoxalase...”
• Pneumococcal galactose catabolism is controlled by multiple regulators acting on pyruvate formate lyase
  Al-Bayati, Scientific reports 2017
  • “...protein 4 SPD_1945 Rod shpae-determining protein MreD, putative 4.6 SPD_1946 Rod shape-determining protein MreC 4.9 SPD_1947 Hypothetical protein 5.5 SPD_1948 ABC transporter, ATP-binding protein 3.7 SPD_1962 Hypothetical protein 11.4 SPD_0116 Hypothetical protein 3.9 SPD_0161 Hypothetical protein 2.6 SPD_0262 PTS system, mannose/fructose/sorbose family protein, IID component 2.3...”
• The Small Molecule DAM Inhibitor, Pyrimidinedione, Disrupts Streptococcus pneumoniae Biofilm Growth In Vitro
  Yadav, PloS one 2015
  • “...regulator DNA binding/sequence-specific DNA binding transcription factor activity transcription, DNA-templated/phosphorelay signal transduction system 1.5 (0.03) SPD_1947 transcriptional regulator, putative sequence-specific DNA binding 3.5 (0.05) SPD_0352 DNA-binding response regulator sequence-specific DNA binding transcription factor activity transcription, DNA-templated 1.4 (0.05) SPD_1049 (lacT) transcription antiterminator LacT RNA binding regulation...”

LLKF_0381 Cro/CI family transcriptional regulator from Lactococcus lactis subsp. lactis KF147
48% identity, 62% coverage

• Strain-Dependent Transcriptome Signatures for Robustness in Lactococcus lactis
  Dijkstra, PloS one 2016
  • “...LLKF_0039 lplL lipoate-protein ligase positive 17.5 LLKF_1293 AMP-dependent synthetase and ligase family protein negative 0.6 LLKF_0381 ydcG Cro/CI family transcriptional regulator positive 5.6 LLKF_1201 nanE N-acetylmannosamine-6-phosphate 2-epimerase positive 0.8 LLKF_0715 glgC glucose-1-phosphate adenylyltransferase catalytic subunit negative 1.6 LLKF_0967 yjgE amino acid transport, ATP-binding protein positive 4.9...”

M6_Spy1106 Transcriptional regulator, Cro/CI family from Streptococcus pyogenes MGAS10394
46% identity, 80% coverage

• Comparative growth, cross stress resistance, transcriptomics of Streptococcus pyogenes cultured under low shear modeled microgravity and normal gravity
  Kalpana, Saudi journal of biological sciences 2016
  • “...protein M6_Spy0984 1.56 Sla M6_Spy0994 1.57 Phage endopeptidase M6_Spy1007 1.53 ATP-dependent Clp protease proteolytic subunit M6_Spy1106 1.56 Transcriptional regulator, Cro/CI family M6_Spy1117 1.50 Hypothetical protein M6_Spy1194 1.52 Unknown phage protein M6_Spy1203 1.66 Hyaluronoglucosaminidase M6_Spy1240 2.66 Unknown phage protein M6_Spy1345 2.07 Unknown phage protein M6_Spy1399 2.01 Hypothetical...”

SPy1386 putative transcriptional regulator protein from Streptococcus pyogenes M1 GAS
46% identity, 86% coverage

• A conserved streptococcal membrane protein, LsrS, exhibits a receptor-like function for lantibiotics
  Biswas, Journal of bacteriology 2014
  • “...last gene of a three-gene operon. The first gene, SPy1386, encodes a putative transcription factor of the HTH XRE superfamily. The second gene, SPy1385, encodes...”
  • “...is the last gene of a threegene operon. SPy1386, which encodes a putative transcriptional regulator protein (71 amino acids) with a helix-turn-helix (HTH) XRE...”

SCA03_05280 helix-turn-helix transcriptional regulator from Streptomyces cacaoi
48% identity, 53% coverage

• Biosynthesis and Heterologous Expression of Cacaoidin, the First Member of the Lanthidin Family of RiPPs
  Román-Hurtado, Antibiotics (Basel, Switzerland) 2021
  • “...permease [ Streptomyces ] 99.65/100 ABC2_membrane_3 (ABC-2 family transporter protein) Cacaoidin biosynthesis caoR3 Hypothetical protein SCA03_05280 [ Streptomyces cacaoi subsp. cacaoi ] 100/100 HTH_XRE domain Negative regulator cao21 Hypothetical protein [ Streptomyces sp. NRRL S-1868] 100/100 No putative conserved domains detected Unknown caoR4 TetR/AcrR family transcriptional...”

lmo0749 lmo0749 from Listeria monocytogenes EGD-e
44% identity, 93% coverage

• A detailed view of the intracellular transcriptome of Listeria monocytogenes in murine macrophages using RNA-seq
  Schultze, Frontiers in microbiology 2015
  • “...Up lmo0576 lmo0576 Hypothetical protein Up lmo0955 lmo0955 Hypothetical protein Up lmo0514 lmo0514 Internalin Up lmo0749 lmo0749 Hypothetical protein Up lmo2102 lmo2102 Glutamine amidotransferase subunit PdxT Down lmo0954 lmo0954 Hypothetical protein Up lmo0748 lmo0748 Hypothetical protein Up lmo0750 lmo0750 Hypothetical protein Up lmo2827 lmo2827 MarR family...”
• The PadR-like transcriptional regulator LftR ensures efficient invasion of Listeria monocytogenes into human host cells
  Kaval, Frontiers in microbiology 2015
  • “...uncharacterized Listeria -specific genes with an interesting exception: the second gene of the operon ( lmo0749 ) is annotated as a transcriptional regulator of the Cro-family of phage proteins, suggesting that LftR and/or other PadR-type proteins could be part of a hierarchical network of transcriptional regulators....”
• Probing the pan-genome of Listeria monocytogenes: new insights into intraspecific niche expansion and genomic diversification
  Deng, BMC genomics 2010
  • “...RpiR family IIIB - - lmo0360 Similar to transcriptional regulator, DeoR family IIIA + - lmo0749 Hypothetical protein IIIA + - lmo0753 Similar to transcription regulator, Crp/Fnr family IIIA - - lmo1030 Similar to transcription regulator, BglG family IIIA + - lmo1060 Similar to 2-component response...”

AF1793 repressor protein from Archaeoglobus fulgidus DSM 4304
48% identity, 86% coverage

• Transcription in archaea
  Kyrpides, Proceedings of the National Academy of Sciences of the United States of America 1999
  • “...AF1022 AF2232 AF0673 AF1270 AF1298 AF1697 AF2136 AF1627 AF1793 AF2425 AF0439 AF0474 AF0584 AF1121 AF1148 AF1404 AF1448 AF1622 AF1723 AF1743 A. fulgidus M....”

CD0370 putative transcriptional regulator from Clostridium difficile 630
50% identity, 91% coverage

• Array comparative hybridisation reveals a high degree of similarity between UK and European clinical isolates of hypervirulent Clostridium difficile
  Marsden, BMC genomics 2010
  • “...protein; putative lantibiotic ABC transporter;ATP-binding protein; two-component system; sensor histidine kinase; two-component system; response regulator CD0370 putative transcriptional regulator CD0381-2 putative conjugative transposon replication initiation factor; putative membrane protein CD0385 putative membrane protein_conjugative transposon protein CD0495 putative regulatory protein (pseudogene) CD0498-9 orf21; orf20 conjugative transposon FtsK/SpoIIIE-family...”

CAC2495 Predicted transcriptional regulator from Clostridium acetobutylicum ATCC 824
48% identity, 94% coverage

• Dynamics of genomic-library enrichment and identification of solvent tolerance genes for Clostridium acetobutylicum
  Borden, Applied and environmental microbiology 2007
  • “...transcriptional regulators (CAC0977, CAC1463, CAC1869, and CAC2495). After subcloning plasmids carrying the CAC0003 and CAC1869 genes, strains 824(pCAC0003)...”
  • “...annotated as transcriptional regulators (CAC0977, CAC1463, CAC1869, and CAC2495) (35). Such genes have the ability to directly or indirectly regulate a large...”

SAG0815 transcriptional regulator, Cro/CI family from Streptococcus agalactiae 2603V/R
47% identity, 85% coverage

• Combining microarray technology and molecular epidemiology to identify genes associated with invasive group B streptococcus
  Zhang, Interdisciplinary perspectives on infectious diseases 2008
  • “...sag0700 925 (97%) 1.0 (0.971.02) 2-dehydro-3-deoxyphosphogluconate aldolase/4-hydroxy-2-oxoglutarate aldolase sag0814 117 (12%) 0.6 (0.390.83) hypothetical protein sag0815 364 (38%) 0.9 (0.761.06) transcriptional regulator, Cro/CI family-related protein sag0832 371 (39%) 1.5 (1.291.77) fibrinogen binding protein sag1130 367 (39%) 1.1 (0.901.25) hypothetical protein sag1140 (b) (b) hypothetical protein sag1207...”

gbs0833 Unknown from Streptococcus agalactiae NEM316
45% identity, 85% coverage

• Extensive adaptive changes occur in the transcriptome of Streptococcus agalactiae (group B streptococcus) in response to incubation with human blood
  Mereghetti, PloS one 2008
  • “...18 transcriptional regulators were down-regulated and 10 were up-regulated ( Table S1 ). For example, gbs0833, gbs1344, gbs1793, gbs1807 and gbs1958, which have homology with the Cro/CI or MerR families of transcriptional regulators, were more than 4-fold up-regulated. Although little is known about the function of...”

SACOL0420 transcriptional regulator, Cro/CI family from Staphylococcus aureus subsp. aureus COL
SAOUHSC_00331 hypothetical protein from Staphylococcus aureus subsp. aureus NCTC 8325
SAUSA300_0350 transcriptional regulator, Cro/CI family-related protein from Staphylococcus aureus subsp. aureus USA300_FPR3757
46% identity, 96% coverage

• Transcriptomic Adjustments of Staphylococcus aureus COL (MRSA) Forming Biofilms Under Acidic and Alkaline Conditions
  Efthimiou, Frontiers in microbiology 2019
  • “...protein 3.22 0.0050 rpoB SACOL05S8 sp| P4776S RPOB_STAAU DNA-directed RNA polymerase beta chain 3.21 0.0010 SACOL0420 ref| NP_388770.1 Predicted transcriptional regulator 3.20 0.0356 mgrA SACOL0746 gb | AAK62673.1 Transcriptional regulator MgrA 3.19 0.0008 Cell wall-Surface tarS SACOL0243 ref| NP_346205-lGlycosyl transferase, family 2:glycosyl transferase family 8 3.28...”
  • “...chain, RpoB), four gene products involved in regulation of transcription (the transcription regulators MgrA, WalR, SACOL0420, and the antiterminator BglG), two capsular biosynthesis enzymes (CapB and CapC), a serine-threonine rich antigen (SasA), two genes associated with methicillin resistance (the essential factor for methicillin resistance, FEMA, and...”
• A putative cro-like repressor contributes to arylomycin resistance in Staphylococcus aureus
  Craney, Antimicrobial agents and chemotherapy 2015
  • “...after every restreak. The spsIB, vraR, and SA0337 (SAOUHSC_00331) genes were amplified using Phusion HF DNA polymerase (New England BioLabs) and the primers...”
  • “...genes, including a putative transcriptional regulator (SAOUHSC_00331) and three putative membrane proteins (SAOUHSC_00332-334). To explore the potential...”
• The Secondary Resistome of Methicillin-Resistant Staphylococcus aureus to β-Lactam Antibiotics
  Abdelmalek, Antibiotics (Basel, Switzerland) 2025 (no snippet)
• A Putative Bacterial ABC Transporter Circumvents the Essentiality of Signal Peptidase
  Morisaki, mBio 2016
  • “...S.aureus ; VISA, vancomycin-intermediate S.aureus . Resistance to compound 103 is caused by mutations in SAUSA300_0350 ( cro / cI ). To determine the mechanism of spontaneous resistance against compound 103, we selected 40 independently generated resistant mutants of S.aureus USA300, which arose at a frequency...”
  • “...revealed that resistance was associated with a single mutation inside or just upstream of gene SAUSA300_0350 in all of these clones. Based on homology to the lambda phage Cro protein, SAUSA300_0350 is annotated as Cro/CI transcriptional regulator-like protein and will be referred to as cro /...”
• Global analysis of transcriptional regulators in Staphylococcus aureus
  Ibarra, BMC genomics 2013
  • “...(28.5%) from B. subtilis. Regulates the transport and degradation of oligomeric beta-glucosides [ 17 ] SAUSA300_0350 Xre YgzD (46%) B. subtilis SAUSA300_0373 Xre No identity to characterized proteins SAUSA300_0503 GntR YdeL (36%) and GabR (32.3%) both from B. subtilis. GabR regulates the expression of GABA synthesis...”

CAC2473 Predicted transcriptional regulator from Clostridium acetobutylicum ATCC 824
48% identity, 77% coverage

• A genomic-library based discovery of a novel, possibly synthetic, acid-tolerance mechanism in Clostridium acetobutylicum involving non-coding RNAs and ribosomal RNA processing
  Borden, Metabolic engineering 2010
  • “...a similar 3-fold higher expression in 824(pRD7) over 824(pSOS95del) as seen in the microarray data. CAC2473, a predicted transcriptional regulator of the xenobiotic-responsive element (XRE) family, with roles in acid tolerance in Lacobacillus acidophilus ( Azcarate-Peril et al., 2004 ) and solvent tolerance in C. acetobutylicum...”

SAPIG0429 helix-turn-helix transcriptional regulator from Staphylococcus aureus subsp. aureus ST398
48% identity, 96% coverage

• Genome-wide high-throughput screening to investigate essential genes involved in methicillin-resistant Staphylococcus aureus Sequence Type 398 survival
  Christiansen, PloS one 2014
  • “...SAPIG2099 428.16 0.00 -inf 0.0237 SAPIG1465 317.79 0.00 -inf 0.0156 SAPIG2108 203.34 0.00 -inf 0.0288 SAPIG0429 196.84 0.00 -inf 0.0298 SAPIG1848 164.21 0.00 -inf 0.0354 SAPIG0633 143.38 0.00 -inf 0.0398 SAPIG0142 726.16 1.10 9.3631 0.0024 SAPIG1650 492.68 1.10 8.8088 0.0128 SAPIG1041 799.62 2.20 8.5048 0.0025 SAPIG1748...”
  • “...synthase Nucleotide and amino acid metabolism (aromatic amino acid metabolism) Oxidative stress and pH shock. SAPIG0429 Hypothetical protein Unknown ? SAPIG2108 Phosphoserine phosphatase, RsbU Up-regulation of B (alternative sigma factor) B influences expression of a variety of genes including virulence genes under stress and specific environmental...”

SA0337 hypothetical protein from Staphylococcus aureus subsp. aureus N315
46% identity, 96% coverage

• An Alternative Terminal Step of the General Secretory Pathway in Staphylococcus aureus
  Craney, mBio 2015
  • “...leader sequences after translocation across the cytoplasmic membrane. Here, we identify the Staphylococcusaureus operon ayrRABC (SA0337 to SA0340) and show that once released from repression by AyrR, the protein products AyrABC together confer resistance to the SPase inhibitor arylomycin M131 by providing an alternate and novel...”
  • “...that S.aureus responds to arylomycin-mediated SPase inhibition by increasing expression of the four adjacent genes, SA0337 to SA0340, and that arylomycin resistance is conferred by loss-of-function mutations in SA0337 ( 15 ). FIG1 AyrR is a transcriptional repressor of itself and three downstream open reading frames....”
• The inhibition of type I bacterial signal peptidase: Biological consequences and therapeutic potential
  Craney, Bioorganic & medicinal chemistry letters 2015
  • “...analysis of the clinical isolates revealed that arylomycin resistance was correlated with the sequence of SA0337, and selection for resistance ex vivo resulted in SA0337 mutations that result in derepression. Further characterization revealed that SA0337 is a Cro-like repressor that controls operon expression, and that the...”
• A putative cro-like repressor contributes to arylomycin resistance in Staphylococcus aureus
  Craney, Antimicrobial agents and chemotherapy 2015
  • “...verified after every restreak. The spsIB, vraR, and SA0337 (SAOUHSC_00331) genes were amplified using Phusion HF DNA polymerase (New England BioLabs) and the...”
  • “...mutant AC0001 was complemented by cloning the wild-type N315 SA0337 (Leu22) and native promoter into the pRB473 vector using the EcoRI and BamHI sites and...”
• Nucleotide substitution and recombination at orthologous loci in Staphylococcus aureus
  Hughes, Journal of bacteriology 2005
  • “...b SA0054 SA0056 SA0057 SA0058 SA0060 SA0222 SA0334 SA0337 SA0349 SA0350 SA0351 SA0382 SA0393 SA0393 SA0408 SA0409 SA0519 SA0521 SA0519 SA0742 SA0840 SA1001...”

EF0869 transcriptional regulator, Cro/CI family from Enterococcus faecalis V583
52% identity, 68% coverage

• A simple and efficient method to search for selected primary transcripts: non-coding and antisense RNAs in the human pathogen Enterococcus faecalis
  Fouquier, Nucleic acids research 2011
  • “...their transcription terminators are spaced by 100nt from translation start codons of the downstream ORFs (Ef0869 and AroE, respectively) transcribed in the same direction, which resembles the organization described for riboswitches or regulatory 5-UTRs ( Figure 4 ), ( 21 ). Although Ref19C and Ref34B RNAs...”
• Transcriptional response of Enterococcus faecalis V583 to erythromycin
  Aakra, Antimicrobial agents and chemotherapy 2005
  • “...Regulatory Regulatory Regulatory Regulatory Regulatory Regulatory EF0129 EF0869 EF1124 EF1303 EF2142 EF2338 EF2544 EF2703 EF2711 EF2966 EF3289 0 0 0.79 0...”

BA1022 DNA-binding protein from Bacillus anthracis str. Ames
43% identity, 79% coverage

• Use of denaturing high-performance liquid chromatography to identify Bacillus anthracis by analysis of the 16S-23S rRNA interspacer region and gyrA gene
  Hurtle, Journal of clinical microbiology 2003
  • “...BA1014 BA1015 BA1016 BA1017 BA1018 BA1019 BA1020 BA1021 BA1022 BA1023 BA1024 BA1025 BA1026 BA1027 BA1030 BA1031 BA1032 BA1033 BA1036, Sterne BA1037 BA1175...”
  • “...thuringiensis thuringiensis thuringiensis thuringiensis BA1015 BA1019 BA1022 BA1023 BA1024 BA1025 SPS Sterne BACI164 BACI165 BACI166 BACI167 BACI168 BACI169...”

MW0325 ORFID:MW0325~hypothetical protein, similar to transcriptional repressor from Staphylococcus aureus subsp. aureus MW2
47% identity, 90% coverage

• Nucleotide substitution and recombination at orthologous loci in Staphylococcus aureus
  Hughes, Journal of bacteriology 2005
  • “...MW0035, MW0037, MW0038, MW0039, MW0041, MW0206, MW0322, MW0325, MW0337, MW0338, MW0339, MW0382, MW0394, MW0395, MW0404, MW0405, MW0516, MW0518, MW0551, MW0764,...”

BLi00946 YazB from Bacillus licheniformis DSM 13
47% identity, 88% coverage

• Pseudomycoicidin, a Class II Lantibiotic from Bacillus pseudomycoides
  Basi-Chipalu, Applied and environmental microbiology 2015
  • “...B. licheniformis DSM13 YgaO (BLi00945) of B. licheniformis DSM13 YgzD (Bli00946) of B. licheniformis DSM13 44 45 62 65 65 65 a Also shown are the percentages of...”

M28_Spy1636 transcriptional regulator, Cro/CI family from Streptococcus pyogenes MGAS6180
46% identity, 88% coverage

• RocA Has Serotype-Specific Gene Regulatory and Pathogenesis Activities in Serotype M28 Group A Streptococcus
  Bernard, Infection and immunity 2018
  • “...M28_Spy1564 M28_Spy1566 M28_Spy1569 M28_Spy1615 M28_Spy1636 M28_Spy1704 M28_Spy1708 M28_Spy1724 M28_Spy1750 M28_Spy1763 M28_Spy1769 M28_Spy1782 M28_Spy1835...”
  • “...scrR M28_Spy1545f M28_Spy1546f srvd,e M28_Spy1566f M28_Spy1569 salRd M28_Spy1636 mgad,e ihkd,e,f ropBd,e ctsRf M28_Spy1763f treRf spxA2d,e ywzGf pipR Known or...”

GTNG_1575 Transcriptional regulator PBSX family from Geobacillus thermodenitrificans NG80-2
40% identity, 94% coverage

• Towards Exploring Toxin-Antitoxin Systems in Geobacillus: A Screen for Type II Toxin-Antitoxin System Families in a Thermophilic Genus
  Alkhalili, International journal of molecular sciences 2019
  • “...genome context. The analysis revealed the presence of a putative gene with the locus tag GTNG_1575, harboring an HTH domain ( Table 1 ). This putative gene is encoded on the opposite DNA strand and is not sharing the operon with a toxin. It has been...”
  • “...solo toxin N.A N.A N.A GNAT GTNG_1578 177 Shared with GTNG_1577 GacA, solo antitoxin HTH GTNG_1575 67 N.A N.A N.A Shared with another protein MazEF RHH GTNG_0206 93 PemK/MazF GTNG_0207 116 Shared Gk GacTA 1 wHTH GK1499 250 GNAT GK1498 144 Separate MazEF (I) AbrB/MazE GK1647...”

Spy49_1597c Putative transcription regulator from Streptococcus pyogenes NZ131
SPy1934 putative transcription regulator from Streptococcus pyogenes M1 GAS
46% identity, 88% coverage

• Identification of novel growth phase- and media-dependent small non-coding RNAs in Streptococcus pyogenes M49 using intergenic tiling arrays
  Patenge, BMC genomics 2012
  • “...Spy49_1592 MOSES18 SR1604140 [ 20 ] a 48 sRNASpy491596c 1574723 1574807 84 - rplM 50S Spy49_1597c L13_leader c 49 sRNASpy491671c 1654859 1654908 49 - emm49 Spy49_1672c a 50 sRNASpy491707c 1693440 1693489 49 - Spy49_1707c Spy49_1708 a 51 sRNASpy491713 1698142 1698191 49 + Spy49_1713 Spy49_1714c SR1719800 [...”
• Application of the random forest algorithm to Streptococcus pyogenes response regulator allele variation: from machine learning to evolutionary models
  Buckley, Scientific reports 2021
  • “...mga2 , lrp , copY , and crgR ], and [ mga2 , lrp , spy1934 , gntR_spy0715 , rivR , M28_spy1337 , spy1325 , gntR_spy1602 , spy1817 , and crgR ], respectively. b AUC=Multiclass classification area under the receiver operating characteristic curve. c Division by...”
  • “...a Ordinary (95.7%) a Regularized (95.2%) a mga2 1 1 1 lrp 2 2 2 spy1934 3 spy0715 ( gntR -like) 4 3 rivR 5 M28_spy1337 6 spy1325 7 spy1602 ( gntR -like) 8 spy1817 9 crgR 10 4 copY 3 The optimal feature set is...”

SAG0251 transcriptional regulator, Cro/CI family from Streptococcus agalactiae 2603V/R
46% identity, 79% coverage

• CsrRS regulates group B Streptococcus virulence gene expression in response to environmental pH: a new perspective on vaccine development
  Santi, Journal of bacteriology 2009
  • “...(SAG0119), coding for the ribose operon repressor; SAG0251, SAG2015, and SAG2037, putative Cro/CI family regulators; SAG0427, a putative MerR family regulator;...”

SXYL_00212 helix-turn-helix transcriptional regulator from Staphylococcus xylosus
43% identity, 92% coverage

• Investigating Extracellular DNA Release in Staphylococcus xylosus Biofilm In Vitro
  Leroy, Microorganisms 2021
  • “...SXYL_01294 dnaG DNA primase 2.2 2.1 SXYL_00005-06 gyrBA DNA gyrase subunits B,A 2.1 * Transcription SXYL_00212 Transcriptional regulator 2.1 2.6 SXYL_00418 marR MarR-family transcriptional regulator 4.1 4.5 SXYL_00690 MarR family transcriptional regulator 3.2 5.1 SXYL_00457 Acetyltransferase 2.5 SXYL_00523 PadR-like family transcriptional regulator 5.9 7.0 SXYL_00786 Transcriptional...”

CD3139 putative transcriptional regulator from Clostridium difficile 630
43% identity, 92% coverage

• Comparative transcriptional analysis of clinically relevant heat stress response in Clostridium difficile strain 630
  Ternan, PloS one 2012
  • “...functions, de-novo thiamine biosynthesis, amino acid metabolism, and several transcriptional regulators (CD1293, CD1292; CD2307, CD2308; CD3139, CD3140) associated with hypothetical proteins were identified. We observed upregulation of genes associated with conversion of pyruvate to acetyl Co-A ( acoA , acoB , acoC , CD0036CD0038), and of...”

BC0690 Transcriptional regulator, PBSX family from Bacillus cereus ATCC 14579
39% identity, 92% coverage

• Recovery of Heat Treated Bacillus cereus Spores Is Affected by Matrix Composition and Factors with Putative Functions in Damage Repair
  Warda, Frontiers in microbiology 2016
  • “...Function Reference B. cereus ATCC 14579 (wild type) + BC0460 + Hypothetical protein This study BC0690 + PbsX family transcriptional regulator This study BC0852 + Quaternary ammonium compound-resistance protein/SugE This study BC0853 + Quaternary ammonium compound-resistance protein/SugE This study BC1312 - a 3-hydroxybutyryl-CoA dehydratase This study...”
  • “...these genes on recovery and possibly damage repair were media independent. In contrast, deletion of BC0690 resulted in higher recovery compared to the wild type in both BHI broth (50% increase) and on BHI agar plates (150% increase) ( Figures 3A,C ). Deletion of cdnL1 (BC4714)...”

SM12261_0720 helix-turn-helix transcriptional regulator from Streptococcus mitis NCTC 12261
42% identity, 77% coverage

• Antibodies Reactive to Commensal Streptococcus mitis Show Cross-Reactivity With Virulent Streptococcus pneumoniae Serotypes
  Shekhar, Frontiers in immunology 2018
  • “...division protein FtsH Membrane 71,326 NA a 93 SP0091 ABC transporter; permease protein Membrane 34,545 SM12261_0720 93 SP0092 ABC transporter substrate-binding protein Extracellular 54,485 SM12261_0719 92 SP0102 Glycosyl transferase Membrane 40,703 No significant similarity SP0107 LysM domain protein Extracellular 20,921 SM12261_0703 96 SP0117 Surface protein A...”

SSV_2224 helix-turn-helix transcriptional regulator from Streptococcus sanguinis
42% identity, 77% coverage

• Cloning-independent markerless gene editing in Streptococcus sanguinis: novel insights in type IV pilus biology
  Gurung, Nucleic acids research 2017
  • “...pilT 2229-F1 TGCCAAAGGTCGGTCTATGT amplifying Up SSV_2229 2229-R1 GTTCTTCAATCGTTTTCGTCATTTTTTCTATCCATTTCTATTGTCGCTT amplifying Up SSV_2229 2224-F2 TTTTACTGGATGAATTGTTTTAGCTTTGAACTCAGACAGAAAGGGG amplifying Dn SSV_2224 2224-R2 TACACATGATCCCCAGCCAG amplifying Dn SSV_2224 2229-R3 CTTTCTGTCTGAGTTCAAAGTTTTTCTATCCATTTCTATTGTCGCTT splicing Up 2229 and Dn 2224 2224-F3 AATAGAAATGGATAGAAAAACTTTGAACTCAGACAGAAAGGGG splicing Up 2229 and Dn 2224 pilD -F1 CCGTTTTTCGATACCAAGGA amplifying Up pilD pilD -R1 GTTCTTCAATCGTTTTCGTCATAATTTTTCCCTTTTTATACTC...”
  • “...mutant with a sPCR product in which the Up and Dn regions of SSV_2229 and SSV_2224 amplified respectively with 2229-F1/2229-R3 and 2224-F3/2224-R2 (Table 1 ) were spliced together. To construct the missense mutants encoding PilD D116A and PilD D179A variants, we first amplified the pilD gene...”

CPF_1032 DNA-binding protein from Clostridium perfringens ATCC 13124
40% identity, 84% coverage

• Ancient bacteria of the Ötzi's microbiome: a genomic tale from the Copper Age
  Lugli, Microbiome 2017
  • “...13124 99.4 168 1 0 1 168 1 168 95.5 343.6 Hypothetical protein CPER_2013 TADB|4710829 CPF_1032 Clostridium perfringens ATCC 13124 100 69 0 0 1 69 1 69 34 139 DNA-binding protein CPER_2208 TADB|4721113 CPR_0896 Clostridium perfringens SM101 97.2 143 4 0 1 143 1 143...”

LSEI_1967 Transcriptional regulator, xre family from Lactobacillus casei ATCC 334
38% identity, 78% coverage

• Genome sequence and comparative genome analysis of Lactobacillus casei: insights into their niche-associated evolution
  Cai, Genome biology and evolution 2009
  • “...LSEI_1957 Phage-related protein 42 9 LSEI_1965 Hypothetical protein 43 9 LSEI_1966 Hypothetical protein 38 9 LSEI_1967 Hypothetical protein 42 9 LSEI_1968 LexA repressor (EC 3.4.21.88) 43 9 LSEI_1971 Phage protein 39 9 LSEI_1972 Hypothetical protein 35 9 LSEI_1975 Hypothetical protein 35 9 LSEI_1976 Hypothetical protein 35...”

CD2308 putative transcriptional regulator from Clostridium difficile 630
C3L34_12490, HMPREF0220_1282 helix-turn-helix transcriptional regulator from Clostridioides difficile
43% identity, 85% coverage

• Comparative transcriptional analysis of clinically relevant heat stress response in Clostridium difficile strain 630
  Ternan, PloS one 2012
  • “...phage functions, de-novo thiamine biosynthesis, amino acid metabolism, and several transcriptional regulators (CD1293, CD1292; CD2307, CD2308; CD3139, CD3140) associated with hypothetical proteins were identified. We observed upregulation of genes associated with conversion of pyruvate to acetyl Co-A ( acoA , acoB , acoC , CD0036CD0038), and...”
• Recognition of extracellular DNA by type IV pili promotes biofilm formation by Clostridioides difficile
  Ronish, The Journal of biological chemistry 2022
  • “...bounded by two conserved genes, OmpR (C3L34_12455 and HMPREF0220_1291) and an unnamed putative transcription factor (C3L34_12490 and HMPREF0220_1282). Recombination in the region between these two genes results in the appearance of pilW in R20291, while no T4P subunits appear in this region of the NAP08 genome....”
  • “...two conserved genes, OmpR (C3L34_12455 and HMPREF0220_1291) and an unnamed putative transcription factor (C3L34_12490 and HMPREF0220_1282). Recombination in the region between these two genes results in the appearance of pilW in R20291, while no T4P subunits appear in this region of the NAP08 genome. TableS1 lists...”

CAC1463 Predicted transcriptional regulator from Clostridium acetobutylicum ATCC 824
48% identity, 75% coverage

• Dynamics of genomic-library enrichment and identification of solvent tolerance genes for Clostridium acetobutylicum
  Borden, Applied and environmental microbiology 2007
  • “...These genes include four transcriptional regulators (CAC0977, CAC1463, CAC1869, and CAC2495). After subcloning plasmids carrying the CAC0003 and CAC1869 genes,...”
  • “...operon, 4 are annotated as transcriptional regulators (CAC0977, CAC1463, CAC1869, and CAC2495) (35). Such genes have the ability to directly or indirectly...”

SAG1128 transcriptional regulator, Cro/CI family from Streptococcus agalactiae 2603V/R
40% identity, 92% coverage

• Adaptive response of Group B streptococcus to high glucose conditions: new insights on the CovRS regulation network
  Di, PloS one 2013
  • “...30 minutes of incubation with 55 mM glucose several transcriptional regulators were modulated. In particular, sag1128 , sag2017 , sag0554 , belonging to the putative Cro/CI family and sag1749 , sag1655 , sag0427 , being part of the putative Mer family of regulators, were 25 fold...”
• Genetic islands of Streptococcus agalactiae strains NEM316 and 2603VR and their presence in other Group B streptococcal strains
  Herbert, BMC microbiology 2005
  • “...and sag1585 Transporters sag1517, sag1998-90, sag1902 and sag1934 Regulators sag0048, sag0124, sag0169, sag 0637, sag0644, sag1128, sag1332, sag1359, sag1409 ( rogB ), sag1463 (encoding a RALP) , sag1791, and sag1956-7 ( rgf ) Encoding other proteins sag0031, sag 0624, sag0662 ( cyl operon), sag0664 ( cyl...”

ID870_03750 helix-turn-helix transcriptional regulator from Streptococcus agalactiae CJB111
40% identity, 76% coverage

• Genomic Analyses Identify Manganese Homeostasis as a Driver of Group B Streptococcal Vaginal Colonization
  Burcham, mBio 2022
  • “...regulator 9.51 7.83 8.05 ID870_02815 pyrR Transcriptional regulator 4.35 ID870_03090 TetR/AcrR family transcriptional regulator 8.59 ID870_03750 Helix-turn-helix transcriptional regulator 6.92 6.59 9.99 ID870_04400 Spx/MgsR family RNA polymerase-binding regulatory protein 6.29 6.05 4.13 5.68 ID870_05775 FadR family transcriptional regulator 6.22 8.42 10.78 9.33 13.07 ID870_06770 ArgR family...”

DR2259 transcriptional regulator, HTH_3 family from Deinococcus radiodurans R1
41% identity, 77% coverage

• Characteristics of dr1790 disruptant and its functional analysis in Deinococcus radiodurans
  Cheng, Brazilian journal of microbiology : [publication of the Brazilian Society for Microbiology] 2015
  • “...DR1916 DNA helicase RecG (recG) 2.543044 0.011 DR1359 ABC-type metal ion transport system 2.518423 0.060 DR2259 Transcriptional regulator 2.45463 0.017 DRA0061 Permease MDR-type 2.111218 0.023 DR0610 P-loop ATPase of adenylate kinase family 2.086652 0.058 DR2213 Conserved hypothetical protein 2.079364 0.024 Locus Annotation Fold increase p value...”

PuuR / VIMSS3563352 PuuR regulator of Spermidine biosynthesis, effector Putrescine from Fervidobacterium nodosum Rt17-B1
35% identity, 36% coverage

CHF17_RS00770 helix-turn-helix transcriptional regulator from Streptococcus agalactiae
39% identity, 87% coverage

• Dual RNA sequencing of group B Streptococcus-infected human monocytes reveals new insights into host-pathogen interactions and bacterial evasion of phagocytosis
  Sullivan, Scientific reports 2023
  • “...protein 31.80 6.61E186 CHF17_RS10785 DUF1304 domain-containing protein 29.84 1.17E37 CHF17_RS08890 Helix-turn-helix transcriptional regulator 15.17 3.80E188 CHF17_RS00770 Helix-turn-helix transcriptional regulator 15.96 2.58E191 CHF17_RS01005 1,4-beta-N-acetylmuramidase 16.26 5.61E115 CHF17_RS06625 Hypothetical protein 16.44 3.74E235 CHF17_RS00720 Hypothetical protein 16.85 6.73E158 CHF17_RS00765 Hypothetical protein 18.75 1.55E253 CHF17_RS00760 Hypothetical protein 20.53 0.00E+00 CHF17_RS00750...”

PuuR / VIMSS5694208 PuuR regulator of Spermidine biosynthesis, effector Putrescine from Thermosipho africanus TCF52B
33% identity, 34% coverage

BA2318 DNA-binding protein from Bacillus anthracis str. Ames
40% identity, 76% coverage

• Detailed genomic analysis of the Wbeta and gamma phages infecting Bacillus anthracis: implications for evolution of environmental fitness and antibiotic resistance
  Schuch, Journal of bacteriology 2006
  • “...set of five contiguous B. anthracis loci were identified (BA2318 to BA2322; Fig. 2B), encoding proteins with 46 to 80% identity to products of the similarly...”
  • “...also encoded within B. anthracis prophage 4066, only at BA2318 to BA2322 is there a stretch of encoded proteins with such extensive sequence similarity. This...”

SAR0704 putative DNA-binding protein from Staphylococcus aureus subsp. aureus MRSA252
38% identity, 50% coverage

• Potential Influence of Staphylococcus aureus Clonal Complex 30 Genotype and Transcriptome on Hematogenous Infections
  Sharma-Kuinkel, Open forum infectious diseases 2015
  • “...(Putative Exported Protein) 1.0 X 1.01E15 CIG149_981 SAR0383 Abi-Like Family Protein 1.9 X 9.77E15 CIG1176_1377 SAR0704 Bacteriophage CI Repressor Helix-Turn-Helix Domain Protein 0.9 X 2.81E14 CIG1524_2315 SAR0697 Bacteriocin Export ABC Transporter 0.9 X 2.81E14 ECTR2_1030 A Haemolytic Family Protein 0.0 X 1.05E13 CIG1165_915 SAR0395 Putative Membrane...”

LMRG_01515 helix-turn-helix transcriptional regulator from Listeria monocytogenes 10403S
40% identity, 93% coverage

• Active Lysogeny in Listeria Monocytogenes Is a Bacteria-Phage Adaptive Response in the Mammalian Environment
  Pasechnek, Cell reports 2020
  • “...two oppositely directed promoters transcribing cI -like and cro -like repressor genes ( LMRG_01514 and LMRG_01515 , respectively) ( Johnson etal., 1981 ; Little etal., 1999 ; Ptashne, 2004 ). Figure2 10403S Transcriptional Response under Lysogenic and Lytic Conditions (A) Schematic representation of the 10403S-genome including...”
  • “...(time 0) and at 1, 3, and 5h post-UV irradiation. Performing this analysis confirmed that LMRG_01515 is a classic Cro-like repressor, which represses the transcription of the early genes in the course of the lytic pathway (including LMRG_02920 and LMRG_01529 ) ( Figure5 A). The function...”

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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.