PaperBLAST

PaperBLAST Hits for CSW01_03560 (86 a.a., MANNKSAKKR...)

Show query sequence

>CSW01_03560
MANNKSAKKRAIQAEKRRQHNASRRSMMRTYMKKTVAAIAAGDKEAATAAFAVVTPILDR
MATKGLIHKNKAARHKSRFFAAINAL

Running BLASTp...

Found 94 similar proteins in the literature:

VC0679 ribosomal protein S20 from Vibrio cholerae O1 biovar eltor str. N16961
100% identity, 100% coverage

• Identification of a chitin-induced small RNA that regulates translation of the tfoX gene, encoding a positive regulator of natural competence in Vibrio cholerae
  Yamamoto, Journal of bacteriology 2011
  • “...also positively regulates several genes (VCA0027, VC1952, VC0679, and VC0972) for extracytoplasmic chitin degradation functions study study study study study...”

B7C60_RS04755 30S ribosomal protein S20 from Vibrio fujianensis
95% identity, 100% coverage

• Comparative Genomics and Transcriptomics Analyses Reveal a Unique Environmental Adaptability of Vibrio fujianensis
  Huang, Microorganisms 2020
  • “...Gene ID Gene Alias Substates Function Upregulated B7C60_RS02450 rpmE large subunit ribosomal protein L31 Translation B7C60_RS04755 rpsT small subunit ribosomal protein S20 Translation B7C60_RS05710 rpmG large subunit ribosomal protein L33 Translation B7C60_RS05715 rpmB large subunit ribosomal protein L28 Translation B7C60_RS11045 rplU large subunit ribosomal protein L21...”

VP0531 ribosomal protein S20 from Vibrio parahaemolyticus RIMD 2210633
94% identity, 100% coverage

• Insights into Vibrio parahaemolyticus CHN25 response to artificial gastric fluid stress by transcriptomic analysis
  Sun, International journal of molecular sciences 2014
  • “...( rpsO ) Chn25_2391 3.7221 30S ribosomal protein S15 VP0266 Chn25_0257 3.3225 Ribosomal protein S17 VP0531 ( rpsT ) Chn25_0481 6.127 30S ribosomal protein S20 Fructose and mannose metabolism VPA1425 Chn25A_1313 23.9303 Mannose-6-phosphate isomerase VP2599 Chn25_2528 0.2922 Fructose-bisphosphate aldolase VP2488 Chn25_2426 4.6724 Putative phosphoglucomutase/phosphomannomutase Amino sugar...”

SG0412 30S ribosomal protein S20 from Sodalis glossinidius str. 'morsitans'
76% identity, 99% coverage

• Quorum sensing primes the oxidative stress response in the insect endosymbiont, Sodalis glossinidius
  Pontes, PloS one 2008
  • “...J ( Figure 3 ). This includes several genes encoding subunits of the 30S (SG0380, SG0412 and SG2269) and 50S ribosomal proteins (SG0133, SG1420, SG1421, SG1572, SG2207, SG2252, SG2270, SG2271 and SG2273). In addition, genes encoding a 16S rRNA pseudouridylate synthase A (SG1570), a tRNA/rRNA methyltransferase...”

A0KG36 Small ribosomal subunit protein bS20 from Aeromonas hydrophila subsp. hydrophila (strain ATCC 7966 / DSM 30187 / BCRC 13018 / CCUG 14551 / JCM 1027 / KCTC 2358 / NCIMB 9240 / NCTC 8049)
80% identity, 99% coverage

• Mechanisms of low susceptibility to the disinfectant benzalkonium chloride in a multidrug-resistant environmental isolate of Aeromonas hydrophila
  Chacón, Frontiers in microbiology 2023
  • “...starvation protein B 0.729 0.018 A0KPW7 UDP-3-O-acyl-N-acetylglucosamine deacetylase 0.958 0.014 A0KLM1 4-hydroxyphenylpyruvate dioxygenase 1.162 0.001 A0KG36 30S ribosomal protein S20 0.0718 0.004 A q -value of < 0.05 corresponds to adjusted p -values after false discovery rate control (FDR). In Figure 6 , we show a...”
  • “...A0KEG2 tatD 4 A0KEE2 purE-1 1 A0KEH0 trx 0 A0KG16 mdh 2 A0KEP0 AHA_0172 0 A0KG36 rpsT 0 A0KEX0 def-1 1 A0KGC5 AHA_0773 0 A0KEX9 AHA_0267 3 A0KGK5 AHA_0854 0 A0KF28 rplP 0 A0KGR3 AHA_0916 4 A0KFH8 AHA_0471 5 A0KHA8 AHA_1118 0 A0KFH9 cyaY 1 A0KHC8...”

FTH_0066 ribosomal protein S20 from Francisella tularensis subsp. holarctica OSU18
69% identity, 96% coverage

• Use of magnetic hydrazide-modified polymer microspheres for enrichment of Francisella tularensis glycoproteins
  Horák, Soft matter 2012
  • “...FTH_0038 Probable multidrug efflux pump 37.24/9.17 CM TMH FTH_0039 Putative uncharacterized protein 15.30/5.16 ? SPII FTH_0066 30S ribosomal protein S20 10.15/10.96 cyt cyt FTH_0067 Elongation factor 4 65.57/5.42 CM cyt FTH_0108 Conserved protein PdpC 156.00/9.17 cyt cyt FTH_0117 Conserved protein (conserved protein PdpB) 127.47/9.63 OM cyt...”
  • “...FTH_0039 Putative uncharacterized protein 15.30/5.16 ? SPII FTH_0038 Probable multidrug efflux pump 37.24/9.17 CM TMH FTH_0066 30S ribosomal protein S20 10.15/10.96 cyt cyt FTH_0091 Putative uncharacterized protein 13.77/5.03 cyt cyt FTH_0105 Intracellular growth locus C protein 22.38/5.65 ? cyt FTH_0108 Conserved protein PdpC 156.00/9.17 cyt cyt...”

HI0965 30S ribosomal protein S20 from Haemophilus influenzae Rd KW20
67% identity, 99% coverage

• Initial proteome analysis of model microorganism Haemophilus influenzae strain Rd KW20
  Kolker, Journal of bacteriology 2003
  • “...HI0581 HI0799 HI0791 HI1468 HI0204 HI0786 HI0545 HI0781 HI0965 HI0531 HI0516 HI0780 HI0777 HI0778 HI0790 HI0793 HI0641 HI0544 HI0640 HI0517 HI1443 HI0788 HI0797...”
• Gene expression changes triggered by exposure of Haemophilus influenzae to novobiocin or ciprofloxacin: combined transcription and translation analysis
  Gmuender, Genome research 2001
  • “...No. hi0567 hi1264 hi1365 hi0070 hi0749 hi1349 hi0750 hi0965 hi1188 hi0249 hi0715 hi0313 hi0459 hi1392 hi0332 hi0623 hi0330 hi0312 hi0713 hi0394 hi1125 hi0250...”

SupS / b0023 30S ribosomal subunit protein S20 from Escherichia coli K-12 substr. MG1655 (see 28 papers)
rpsT / P0A7U7 30S ribosomal subunit protein S20 from Escherichia coli (strain K12) (see 26 papers)
RS20_ECOLI / P0A7U7 Small ribosomal subunit protein bS20; 30S ribosomal protein S20 from Escherichia coli (strain K12) (see 8 papers)
rpsT / EW|b0023 30S ribosomal protein S20 from Escherichia coli K12 (see 13 papers)
ECs0026 30S ribosomal subunit protein S20 from Escherichia coli O157:H7 str. Sakai
NP_414564 30S ribosomal subunit protein S20 from Escherichia coli str. K-12 substr. MG1655
b0023 30S ribosomal protein S20 from Escherichia coli str. K-12 substr. MG1655
c0027 30S ribosomal protein S20 from Escherichia coli CFT073
S0022 30S ribosomal protein S20 from Shigella flexneri 2a str. 2457T
Z0027 30S ribosomal subunit protein S20 from Escherichia coli O157:H7 EDL933
Z_RS00125 30S ribosomal protein S20 from Escherichia coli O157:H7 str. EDL933
71% identity, 99% coverage

• function: Binds directly to 16S ribosomal RNA
  subunit: Part of the 30S ribosomal subunit (PubMed:10094780, PubMed:12244297, PubMed:12809609, PubMed:16272117, PubMed:27906160, PubMed:27906161, PubMed:27934701, PubMed:786731).
• Global transcriptional response of Escherichia coli O157:H7 to growth transitions in glucose minimal medium
  Bergholz, BMC microbiology 2007
  • “...mogA 2.27 2 ECs0526 htpG -2.70 1 ECs0015 dnaJ -2.32 1 ECs0527 adk -3.22 1 ECs0026 rpsT -4.14 1 ECs0540 O157 3.52 2 ECs0028 ribF -2.36 1 ECs0541 O157 4.11 2 ECs0029 ileS -2.81 1 ECs0552 ybbK 3.00 2 ECs0030 lspA -2.38 1 ECs0561 ybbD 2.16...”
• Assembly of the 5' and 3' minor domains of 16S ribosomal RNA as monitored by tethered probing from ribosomal protein S20.
  Dutca, Journal of molecular biology 2008
  • GeneRIF: These results suggest that the two domains of 16S ribosomal RNA, 5' and 3' minor, are organized relative to S20 at different stages of assembly.
• Primary structure of protein S20 from the small ribosomal subunit of Escherichia coli.
  Wittmann-Liebold, FEBS letters 1976 (PubMed)
  • GeneRIF: N-terminus verified by Edman degradation on mature peptide
• Capturing Membrane Protein Ribosome Nascent Chain Complexes in a Native-like Environment for Co-translational Studies
  Pellowe, Biochemistry 2020
  • “...RS13, P0A7S9; RS14, P0AG59; RS15, P0ADZ4; RS16, P0A7T3; RS17, P0AG63; RS18, P0A7T7; RS19, P0A7U3; RS20, P0A7U7; RS21, P68681; RS22, C8U8F3. Large ribosomal subunits (50S): RL1, P0A7L0; RL2, P60422; RL3, P60438; RL4, P60723; RL5, P62399; RL6, P0AG55; RL7, P0A7K2; RL9, P0A7R1; RL10, P0A7J3; RL11, P0A7J7; RL13, P0AA10;...”
• Proteomic Study of the Survival and Resuscitation Mechanisms of Filamentous Persisters in an Evolved Escherichia coli Population from Cyclic Ampicillin Treatment
  Sulaiman, mSystems 2020
  • “...3.32 P0A799 pgk Phosphoglycerate kinase 0.023 3.36 P0A917 ompX Outer membrane protein X 0.029 4.33 P0A7U7 rpsT 30S ribosomal protein S20 0.006 4.54 Knockout of elaB increases persistence and leads to small colony variant (SCV) formation after ampicillin treatment. One of the most upregulated proteins in...”
• A coordinated proteomic approach for identifying proteins that interact with the E. coli ribosomal protein S12
  Strader, Journal of proteome research 2013
  • “...P0AG63 S17 10 274 65.1 P0A7T7 S18 10 520 84 P0A7U3 S19 10 339 70.6 P0A7U7 S20 8 225 60.9 P68679 S21 7 231 34.7 P60422 L2 12 111 43.3 P60438 L3 3 24 22.9 P60723 L4 5 55 32.8 P62399 L5 10 68 58.1 P0AG55...”
  • “...S15 8 90 68.5 8 36 60 P0A7T7 S18 5 63 50.6 5 99 50.6 P0A7U7 S20 4 22 55.2 ** B. Candidate S12 binders from polysome-free (PDE) mid-log and stationary Midlog Sationary Acession Protein Name Unique Matched % Seq. Unique Matched % Seq. Peptides Spectra...”
• A proteomic and transcriptomic approach reveals new insight into beta-methylthiolation of Escherichia coli ribosomal protein S12
  Strader, Molecular & cellular proteomics : MCP 2011
  • “...P0A7V8 P0A7W1 P02358 P02359 P0A7W7 P0A7X3 P0A7R5 P0A7R9 P0A7S3 P0A7S9 P0ADZ4 P0A7T7 P0A7U7 S1 S4 S5 S6 S7 S8 S9 S10 S11 S12 S13 S15 S18 S20 27 17 29 9 15 10 8 5...”
• Global transcriptomic analysis of an engineered Escherichia coli strain lacking the phosphoenolpyruvate: carbohydrate phosphotransferase system during shikimic acid production in rich culture medium
  Cortés-Tolalpa, Microbial cell factories 2014
  • “...of acid-resistance protein Stress response 32.4174 hdeB b3509 Polypeptide: acid stress chaperone Stress response 56.2185 b0023 b0023 Polypeptide: 30S ribosomal subunit protein S20 Structural molecule activity 45.8728 cysC b2750 Enzyme: adenylylsulfate kinase Sulfur metabolism 52.8463 cysD cysD Polypeptide: CysD Sulfur metabolism 236.2573 cysH b2762 Enzyme: 3-phospho-adenylylsulfate...”
• A comparison of key aspects of gene regulation in Streptomyces coelicolor and Escherichia coli using nucleotide-resolution transcription maps produced in parallel by global and differential RNA sequencing
  Romero, Molecular microbiology 2014
  • “...mRNAs. (A), (B), (C), (D) and (E) show annotated views of the E. coli rpsT (b0023), ompA (b0957), eno (b2779), pnp (b3165) and adhE (b1241) respectively. The tracks from top to bottom show the genome positions, gRNA-seq reads, gene locations and differential RNA-seq reads (in the...”
• Remaining flexible in old alliances: functional plasticity in constrained mutualisms
  Wernegreen, DNA and cell biology 2009
  • “...rpsJ b3321 Bpen197 Bfl190 WGLp542 BU525 BUsg506 Bbp468 rpsT b0023 Bpen120 Bfl116 WGLp296 BU151 BUsg144 Bbp140 rseP (yaeL) b0176 Bpen286 Bfl278 WGLp385 - - -...”
• Global analysis of extracytoplasmic stress signaling in Escherichia coli
  Bury-Moné, PLoS genetics 2009
  • “...enzyme IIA component -; -; 1.9; -; 1.5 ycbZ b0955 Putative ATP-dependent protease 1.9 rpsT b0023 30S ribosomal protein S20 2.0 yciG yciF yciE b1259-7 YciF: putative structural protein, osmotically induced, belong to the S regulon -; 2.2; - endA b2945 DNA-specific endonuclease I 2.4 ybcU...”
• Analysis of promoter targets for Escherichia coli transcription elongation factor GreA in vivo and in vitro
  Stepanova, Journal of bacteriology 2007
  • “...of wt GreA (fold) Gene description or function b0023 2 30S ribosomal subunit protein S20 aceE aceF b0114 Z0125 4.9 4.9 Pyruvate dehydrogenase (decarboxylase...”
• A functional update of the Escherichia coli K-12 genome
  Serres, Genome biology 2001
  • “...f Protein chain elongation factor EF-Ts b0236 ec_0334 prfH pf Putative peptide chain release factor b0023 ec_0031 rpsT s 30S ribosomal subunit protein S20 b0138 ec_0200 yadM ps Putative fimbrial-like protein b0684 ec_1032 fldA c Flavodoxin 1 b1697 ec_2618 ydiQ pc Putative electron transfer flavoprotein b0251...”
• Combined, functional genomic-biochemical approach to intermediary metabolism: interaction of acivicin, a glutamine amidotransferase inhibitor, with Escherichia coli K-12
  Smulski, Journal of bacteriology 2001
  • “...b3230 b3321 b3297 b3298 b3307 b2609 b3311 b4202 b3316 b0023 b3065 b3175 b0146 b3908 b0120 b2533 b0053 b0002 b2607 b1265 b4054 b1637 b1617 b1616 b1184 b2498...”
• Genome-wide transcriptional profiling of the Escherichia coli responses to superoxide stress and sodium salicylate
  Pomposiello, Journal of bacteriology 2001
  • “...J. BACTERIOL. TABLE 2--Continued Gene type b Gene Ratio b3316 b0023 b0121 b4240 b2607 b3384 b0170 b3339 b2014 rpsS rpsT speE treB trmD trpS tsf tufA yeeF 0.2...”
• Emergence of Plasmid-Borne dfrA14 Trimethoprim Resistance Gene in Shigella sonnei
  Miranda, Frontiers in cellular and infection microbiology 2016
  • “...New England Biolabs ); lane 2, E. coli 39R861; lane 3 4, S. sonnei strain c0027 and the respective TMP R E. coli DH5 transformant; lane 5 6, S. sonnei strain c0700 and the TMP R transformant; lane 7 8, S. sonnei strain c0719 and the...”
• Individual and Combined Effects of 2′-Fucosyllactose and Bifidobacterium longum subsp. infantis on the Gut Microbiota Composition of Piglets
  Wang, The Journal of nutrition 2024
• Gut Microbes and Circulating Cytokines in Preterm Infants with Growth Failure
  Strobel, The Journal of nutrition 2023 (secret)
• The genetic and bacteriological aspects of Peyronie's disease
  Ralph, The Journal of urology 1997 (PubMed) (secret)
• Transcriptional responses of Escherichia coli K-12 and O157:H7 associated with lettuce leaves
  Fink, Applied and environmental microbiology 2012
  • “...Z5809 Z4676 Z4692 Z4667 Z4700 Z4668 Z4677 Z4526 Z3903 Z5811 Z0027 Z4418 Z2230 Z1864 rimP rplA rplB rplD rplE rplF rplK rplM rplN rplR rplW rplX rplY rpmB rpmG...”
• Transcriptomic Analysis of Viable but Non-Culturable Escherichia coli O157:H7 Formation Induced by Low Temperature
  Zhong, Microorganisms 2019
  • “...rps S, rpm D, Z_RS20780, rps J, Z_RS27210, rpl J, rpl Q, Z_RS27195, rpl O, Z_RS00125, Z_RS30885 Related protein annotations Differentially expressed genes of significant protein annotation in the signal pathway RNA Polymerase Subunit and (+) Subunit : rpl Q, rpl M, rps I; Subunit :...”

HSM_0741 30S ribosomal protein S20 from Histophilus somni 2336
HSM_0741 30S ribosomal protein S20 from Haemophilus somnus 2336
67% identity, 99% coverage

• Identification and initial characterization of Hfq-associated sRNAs in Histophilus somni strain 2336
  Subhadra, PloS one 2023
  • “...287 Y Y HSM_0708 HSM_0709 ND This work HS67 851529 851687 158 Y Y HSM_0740 HSM_0741 B [ 8 ] HS70 869792 869984 193 Y Y HSM_0751 HSM_0752 ND This work HS72 876309 876450 142 Y Y HSM_0658 HSM_0659 C [ 8 ] HS78 969506 969784...”

NP_459048 30S ribosomal subunit protein S20 from Salmonella enterica subsp. enterica serovar Typhimurium str. LT2
P0A2B1 Small ribosomal subunit protein bS20 from Salmonella typhimurium (strain LT2 / SGSC1412 / ATCC 700720)
SEN0043 30S ribosomal protein S20 from Salmonella enterica subsp. enterica serovar Enteritidis str. P125109
SC0037 30S ribosomal subunit protein S20 from Salmonella enterica subsp. enterica serovar Choleraesuis str. SC-B67
SENTW_4750 30S ribosomal protein S20 from Salmonella enterica subsp. enterica serovar Weltevreden str.
70% identity, 99% coverage

• Mutational robustness of ribosomal protein genes.
  Lind, Science (New York, N.Y.) 2010 (PubMed)
  • GeneRIF: fitness effects of a large number of defined single mutations in rpsT and rplA were measured; distribution of fitness effects (DFE) appears unimodal, where most mutations are weakly deleterious and remaining ones are potentially neutral
• N-dodecanoyl-homoserine lactone influences the levels of thiol and proteins related to oxidation-reduction process in Salmonella
  de, PloS one 2018
  • “...Translation 0.149 0.404 ND ND ND ND ND ND ND ND 30S ribosomal protein S20 P0A2B1 rpsT Translation 1.295 4.181 1.915 1.348 0.834 1.072 1.105 0.776 -1.148 1.054 Elongation factor P P64036 efp Translation -9.275 1.432 ND ND ND ND ND ND ND ND Elongation factor...”
• Global transcriptomic analysis of ethanol tolerance response in Salmonella Enteritidis
  He, Current research in food science 2022
  • “...L4 SEN3550 rpmB 2.40 50S ribosomal protein L28 SEN3263 rplV 4.37 50S ribosomal protein L22 SEN0043 rpsT 3.49 30S ribosomal protein S20 SEN3935 rplJ 3.32 50S ribosomal protein L10 SEN2594 rplS 3.71 50S ribosomal protein L19 SEN3250 rpmD 4.40 50S ribosomal protein L30 SEN1708 rplT 2.80...”
• Prevalence and characterization of genotypic diversity of Haemophilus parasuis isolates from southern China
  Zhang, Canadian journal of veterinary research = Revue canadienne de recherche veterinaire 2012 (secret)
• Transcriptional profile of Salmonella enterica subsp. enterica serovar Weltevreden during alfalfa sprout colonization
  Brankatschk, Microbial biotechnology 2014
  • “...rpsR SENTW_4496 12.63 30S ribosomal protein S18 rpsS SENTW_3563 7.07 30S ribosomal protein S19 rpsT SENTW_4750 6.53 30S ribosomal protein S20 rpsU SENTW_3346 9.92 30S ribosomal protein S21 yfjA SENTW_2839 5.16 Ribosome maturation factor RimM Unclassified yaiB SENTW_0366 5.03 Anti-adapter protein IraP nusG SENTW_4257 5.15 Elongation...”

PMCN03_2059 30S ribosomal protein S20 from Pasteurella multocida subsp. multocida str. HB03
67% identity, 99% coverage

• Genomic and transcriptomics analysis reveal putative secreted proteins expressed of <i>Pasteurella multocida</i> during 18β-glycyrrhetinic acid treatment
  Wu, Frontiers in veterinary science 2024
  • “...36 PMCN03_1970 50S ribosomal protein L1, rpl11 37 PMCN03_1971 50S ribosomal protein L1, rpl1 38 PMCN03_2059 30S ribosomal protein S20, rps20 39 PMCN03_0319 Sel1-like protein 40 PMCN03_1641 xynC protein 3.2 Functional annotations analysis of putative secreted proteins To classify the putative secreted proteins with a common...”

8a3lT / P0A7U7 8a3lT (see paper)
71% identity, 99% coverage

• Ligand: rna (8a3lT)

PA4563 30S ribosomal protein S20 from Pseudomonas aeruginosa PAO1
67% identity, 95% coverage

• Transcriptional and proteomic responses of Pseudomonas aeruginosa PAO1 to spaceflight conditions involve Hfq regulation and reveal a role for oxygen
  Crabbé, Applied and environmental microbiology 2011
  • “...PA4351 PA4352 PA4386 PA4425 PA4430 PA4431 PA4432 PA4433 PA4482 PA4563 PA4568 ldh PA3440 rhlI rhlA PA3520 bfrB PA3575 fdxA lpxA fabZ lpxD tsf rpsB adk PA3723...”
• Indole and 7-hydroxyindole diminish Pseudomonas aeruginosa virulence
  Lee, Microbial biotechnology 2009
  • “...1.1 Probable antioxidant protein PA3721 nalC 3.0 1.1 1.6 Transcriptional regulator NalC, induced by MvfR PA4563 rpsT 2.8 2.8 1.1 30S ribosomal protein S20 Hypothetical proteins PA0284 13.9 1.6 1.2 Hypothetical protein, induced by MvfR PA0492 4.3 3.5 1.9 Hypothetical protein PA0696 4.3 2.5 1.3 Hypothetical...”
• Transcriptome analysis reveals that multidrug efflux genes are upregulated to protect Pseudomonas aeruginosa from pentachlorophenol stress
  Muller, Applied and environmental microbiology 2007
  • “...Metabolism PA1588 (sucC) PA2951 (etfA) PA3814 (iscS) PA4443 (cysD) PA4563 (rpsT) PA4748 (tpiA) PA4847 (accB) PA5013 (ilvE) PA5570 (rpmH) 13 h c VOL. 73, 2007...”
• Microarray analysis of Pseudomonas aeruginosa reveals induction of pyocin genes in response to hydrogen peroxide
  Chang, BMC genomics 2005
  • “...), and PA3607-3610 ( potABCD ), and (iii) ribosomal protein genes, PA4432 ( rpsL ), PA4563 ( rpsT ), PA5049 ( rpmE ), and PA5315 ( rpmG ). It is also interesting that putative cell division inhibitors such as PA0671 and PA3008, which are similar to...”
  • “...( potD ) 35.4 105.9 0.008 -3.0 PA4432 ( rpsL ) 493.8 1156.9 0.008 -2.3 PA4563 ( rpsT ) 1600.9 3648.5 0.008 -2.3 PA5049 ( rpmE ) 174.9 482.0 0.008 -2.8 PA5315 ( rpmG ) 340.3 761.5 0.008 -2.2 PA0671 127.5 25.4 0.008 5.0 PA3008 618.6...”
• Characterization of nutrient-induced dispersion in Pseudomonas aeruginosa PAO1 biofilm
  Sauer, Journal of bacteriology 2004
  • “...PA0722 PA0720 PA0723 PA1148 PA4853 PA3743 PA4275 PA3656 PA4563 PA2851 PA4268 PA0579 PA2619 PA4432 PA3647 PA1341 PA0282 PA1339 PA0280 PA1340 Regulatory protein...”

EAM_RS03205 30S ribosomal protein S20 from Erwinia amylovora ATCC 49946
EAMY_2940 30S ribosomal protein S20 from Erwinia amylovora CFBP1430
66% identity, 99% coverage

• A complete twelve-gene deletion null mutant reveals that cyclic di-GMP is a global regulator of phase-transition and host colonization in Erwinia amylovora
  Kharadi, PLoS pathogens 2022
  • “...CDS HslUHslV peptidase ATPase subunit 2.186164935 1.37E-27 EAM_RS16210 zinc/cadmium/mercury/lead-transporting ATPase CDS zinc/cadmium/mercury/lead-transporting ATPase 2.142197384 6.38E-17 EAM_RS03205 rpsT CDS 30S ribosomal protein S20 2.067365283 6.13E-05 EAM_RS15625 rplF CDS 50S ribosomal protein L6 2.009381497 3.20E-05 EAM_RS05285 leucine-rich repeat domain-containing protein CDS leucine-rich repeat domain-containing protein -4.528529394 1.91193E-44 EAM_RS17045...”
• The stringent response regulator (p) ppGpp mediates virulence gene expression and survival in Erwinia amylovora
  Yang, BMC genomics 2020
  • “...rpsO , ribosomal protein S15 2.51 10.25 EAMY_0417 rpsU , ribosomal protein S21 2.12 10.15 EAMY_2940 rpsT , ribosomal protein S20 1.84 10.18 EAMY_2760 rpsB , ribosomal protein S2 1.82 11.96 EAMY_3373 rpsN , ribosomal protein S14 1.76 11.7 EAMY_3372 rpsH , ribosomal protein S8 1.72...”

FXO12_14490 30S ribosomal protein S20 from Pseudomonas sp. J380
65% identity, 93% coverage

• A Novel Marine Pathogen Isolated from Wild Cunners (Tautogolabrus adspersus): Comparative Genomics and Transcriptome Profiling of Pseudomonas sp. Strain J380
  Umasuthan, Microorganisms 2021
  • “...FXO12_18260, rpmH ; FXO12_11415, rpsB ; FXO12_15685, rpsF ; FXO12_22170, rpsH ; FXO12_13405, rpsI ; FXO12_14490, rpsT ; and FXO12_21760, rpsU ), elements or regulators involved in transcription (FXO12_23400, greA ; FXO12_22365, nrdR ; FXO12_22390, nusB ; FXO12_19455, rho ; FXO12_23460, nusA ) and translation (FXO12_02255,...”
  • “...2.79 7.9 10 15 FXO12_21760 Complement (4790073..4790288) rpsU 30S ribosomal protein S21 RpsU 3.24 0 FXO12_14490 3182295..3182573 rpsT 30S ribosomal protein S20 RpsT 3.79 0 Protein Synthesis FXO12_23400 5120014..5120490 greA Transcription elongation factor GreA 1.09 2.2 10 3 FXO12_22365 49025..4903169 nrdR Transcriptional repressor NrdR 1.26 3.3...”

PP0600, PP_0600 ribosomal protein S20 from Pseudomonas putida KT2440
Pput_0641 30S ribosomal protein S20 from Pseudomonas putida F1
65% identity, 93% coverage

• UEG Week 2024 Poster Presentations
  , United European gastroenterology journal 2024
• UEG Week 2023 Poster Presentations
  , United European gastroenterology journal 2023
• H-NS Family Proteins Drastically Change Their Targets in Response to the Horizontal Transfer of the Catabolic Plasmid pCAR1
  Nakamura, Frontiers in microbiology 2020
  • “...ribosomal protein S13 PP_0477 rpsK 30S ribosomal protein S11 PP_0478 rpsD 30S ribosomal protein S4 PP_0600 rpsT 30S ribosomal protein S20 PP_0689 rpmA 50S ribosomal protein L27 PP_1462 rpsP 30S ribosomal protein S16 PP_1463 rim 16S rRNA-processing protein RimM PP_1496 lysS Lysyl-tRNA synthetase PP_1911 rpmF 50S...”
• Mechanisms of resistance to chloramphenicol in Pseudomonas putida KT2440
  Fernández, Antimicrobial agents and chemotherapy 2012
  • “...PP0378 (M) PP0379 (M) PP0380 PP0389 PP0491 PP0560 PP0600 PP0601 PP0626 PP1868 (M) PP1911 PP1935 PP2320 PP2644 PP2645 PP2663 (M) PP2664 PP2665 (M) PP2666...”
• iTRAQ-based quantitative proteomic analysis of the global response to 17β-estradiol in estrogen-degradation strain Pseudomonas putida SJTE-1
  Xu, Scientific reports 2017
  • “...gi|148548674 Bacterial nucleoid protein HU beta subunit Pput_3466 1.60 0.038 gi|148545891 30S ribosomal protein S20 Pput_0641 1.65 0.001 gi|148545741 50S ribosomal protein L23 Pput_0489 1.80 0.040 gi|148546196 Diguanylate cyclase/phosphodiesterase Pput_0953 2.93 0.024 gi|148545967 50S ribosomal protein L27 Pput_0721 0.60 0.008 gi|148546471 Ribosomal S12 methylthiotransferase RimO Pput_1228...”

VT47_03545 30S ribosomal protein S20 from Pseudomonas syringae pv. syringae
65% identity, 93% coverage

• Identification of the Genes of the Plant Pathogen Pseudomonas syringae MB03 Required for the Nematicidal Activity Against Caenorhabditis elegans Through an Integrated Approach
  Ali, Frontiers in microbiology 2022
  • “...availability. Additionally, pntA (VT47_24115) and scoB (VT47_15125) were up-regulated, whereas scoP (V47_01435), queD (VT47_04670), rpsT (VT47_03545), and two hypothetical proteins (VT47_13300, VT47_14685) were down-regulated during hostpathogen interaction regardless of the bacterial growth phase ( Supplementary Table 5 ). FIGURE 3 Heatmap showing differential expression of bacterial...”

ACIAD1389 30S ribosomal protein S20 from Acinetobacter sp. ADP1
64% identity, 97% coverage

• iTRAQ-Based Comparative Proteomic Analysis of Acinetobacter baylyi ADP1 Under DNA Damage in Relation to Different Carbon Sources
  Jiang, Frontiers in microbiology 2019
  • “...0.44 0.65 Protein RecA recA ACIAD1385 0.57 0.51 0.59 0.45 30S ribosomal protein S20 rpsT ACIAD1389 0.21 0.35 0.25 0.29 tRNA (uracil-5-)-methyltransferase trmA ACIAD1645 0.28 0.52 0.41 0.34 Tellurium resistance protein terX ACIAD1968 0.68 0.65 0.81 0.7 DNA polymerase III beta dnaX ACIAD1970 0.78 0.37 0.6...”

A1S_1617 30S ribosomal protein S20 from Acinetobacter baumannii ATCC 17978
62% identity, 98% coverage

• Effects of Sub-Minimum Inhibitory Concentrations of Imipenem and Colistin on Expression of Biofilm-Specific Antibiotic Resistance and Virulence Genes in Acinetobacter baumannii Sequence Type 1894
  Shenkutie, International journal of molecular sciences 2022
  • “...protein Transcription and translation E5A72_RS17735 acb: A1S_1974 6.5036 3.9244 2.1244 Ribosome releasing factor Novel00584 acb: A1S_1617 5.4437 3.7365 3.01 30S ribosomal protein S20 Novel00490 - 7.0401 1.1587 0.415 Transcription termination factor Rho OS E5A72_RS04400 acb: A1S_3029 3.4737 2.161 2.4156 tRNA-Arg Peptidoglycan biosynthesis E5A72_RS10790 acb: A1S_1965 1.6823...”
  • “...1572 DNA replication E5A72_RS17735 acb: A1S_1974 Ribosome releasing factor 3685962 3686516 555 Translation Novel00584 acb: A1S_1617 30S ribosomal protein S20 3284582 3284881 300 Novel00490 - Transcription termination factor Rho OS 2214580 2215974 1395 Transcription E5A72_RS14510 acb: A1S_1359 ABC 3 -type Fe 3+ transport system + 3025424...”
• Whole transcriptome analysis of Acinetobacter baumannii assessed by RNA-sequencing reveals different mRNA expression profiles in biofilm compared to planktonic cells
  Rumbo-Feal, PloS one 2013
  • “...symporter 0.29 1.03 A1S_1541 hypothetical protein 8.27 9.19 A1S_1572 30S ribosomal protein S1 1.74 0.88 A1S_1617 30S ribosomal protein S20 4.08 1.15 A1S_1631 iron-binding protein 0.71 0.13 A1S_1637 DNA-binding protein HU-beta 1.13 5.12 A1S_1657 siderophore biosynthesis protein 13.61 2.89 A1S_1687 transcriptional regulator 1.84 0.00 A1S_1726 aspartate...”

7m4ut / B7I5N9 A. Baumannii ribosome-eravacycline complex: 30s (see paper)
61% identity, 99% coverage

• Ligand: rna (7m4ut)

8rdvTo / A0A0M4T3R2 8rdvTo (see paper)
60% identity, 98% coverage

• Ligand: rna (8rdvTo)

APL_1558 30S ribosomal protein S20 from Actinobacillus pleuropneumoniae L20
66% identity, 99% coverage

• Actinobacillus pleuropneumoniae genes expression in biofilms cultured under static conditions and in a drip-flow apparatus
  Tremblay, BMC genomics 2013
  • “...APL_0333 APL_0615 APL_0630 APL_0644 APL_0682 APL_0771 APL_0903 APL_0967 APL_0982 APL_1136 APL_1169 APL_1292 APL_1388 APL_1450 APL_1474 APL_1558 APL_1597 APL_1759 APL_1782 APL_1962 Interestingly, APL_1494, which encodes the fine tangled pili,was down-regulated in the drip-flow biofilm and in bacteria attached to SJPL cells [ 19 ]. This gene was...”
• Host-pathogen interactions of Actinobacillus pleuropneumoniae with porcine lung and tracheal epithelial cells
  Auger, Infection and immunity 2009
  • “...B Tyrosyl-tRNA synthetase 50S ribosomal protein L19 APL_1558 APL_1765 APL_0566 APL_1400 APL_0487 APL_1762 APL_1763 APL_1761 APL_0223 APL_1773 APL_1775 APL_0399...”

lpg2636 30S ribosomal protein S20 from Legionella pneumophila subsp. pneumophila str. Philadelphia 1
lpp2689 30S ribosomal subunit protein S20 from Legionella pneumophila str. Paris
58% identity, 98% coverage

• New Global Insights on the Regulation of the Biphasic Life Cycle and Virulence Via ClpP-Dependent Proteolysis in Legionella pneumophila
  Ge, Molecular & cellular proteomics : MCP 2022
  • “...5.86 3.51 Uncharacterized protein Lpg1810 lpg1810 52.6 6.47 1.21 Long chain fatty acid transporter RpsT lpg2636 9.7 11.36 2.99 30S ribosomal protein S20 Lpg0229 lpg0229 31.8 6.39 Heme oxygenase UppS lpg0503 27.4 6.3 Polycis-undecaprenyl-diphosphate synthase Lpg0732 lpg0732 23.4 6.07 Uncharacterized protein Lpg0839 lpg0839 20.3 5.57 KdsC...”
• Epidemiological information is key when interpreting whole genome sequence data - lessons learned from a large Legionella pneumophila outbreak in Warstein, Germany, 2013
  Petzold, Euro surveillance : bulletin Europeen sur les maladies transmissibles = European communicable disease bulletin 2017
  • “...2974818 NA b YP_096638.1 3 5 5 lpg2635 2976210 2977781 mviN YP_096640.1 1 4 26 lpg2636 2978139 2978405 rpsT YP_096641.1 1 2 2 Differing cgMLST targets of 26kb recombination region (13 targets) lpg2666 3013221 3014102 NA b YP_096671.1 1 4 9 lpg2667 3014236 3015114 rpoH YP_096672.1...”
• Transcriptomic changes of Legionella pneumophila in water
  Li, BMC genomics 2015
  • “...2.09 Translation 30S ribosomal protein S13 lpg0351 rpsM 2.57 4.22 5.00 30S ribosomal protein S20 lpg2636 rpsT 3.86 4.43 6.92 30S ribosomal protein S6 lpg1592 rpsF 2.99 4.18 4.84 30S ribosomal protein S7 lpg0325 rpS7 2.43 3.36 3.89 50S ribosomal protein L15 lpg0348 rplO 1.76 3.37...”
• Two small ncRNAs jointly govern virulence and transmission in Legionella pneumophila
  Sahr, Molecular microbiology 2009
  • “...- lpp2827 NADH-quinone oxidoreductase chain J 2.42 - lpp2768 50S ribosomal protein L35 3.06 2.88 lpp2689 30S ribosomal subunit protein S2 3.33 1.78 lpp2026 Peptidoglycan-associated lipoprotein precursor 1.79 4.52 lpp1958 Major outer membrane protein 2.16 6.57 lpp1773 Similar to long-chain fatty acid transport protein 3.07 3.16...”

PD1440 30S ribosomal protein S20 from Xylella fastidiosa Temecula1
XF2421 30S ribosomal protein S20 from Xylella fastidiosa 9a5c
57% identity, 97% coverage

• Csp1, a Cold Shock Protein Homolog in Xylella fastidiosa Influences Cell Attachment, Pili Formation, and Gene Expression
  Wei, Microbiology spectrum 2021
  • “...0.16 PD0062 fimA Fimbrial subunit precursor 10,009.57 1,724.44 0.17 PD0217 Hypothetical protein 2,815.96 511.29 0.18 PD1440 rpsT 30S ribosomal protein S20 6,060.28 1,246.99 0.21 PD0708 Virulence regulator 672.31 141.02 0.21 PD1914 rpmI 50S ribosomal protein L35 21,603.77 4,619.53 0.21 PD0626 ssb Single-stranded DNA-binding protein 484.98 103.71...”
• Global expression profile of biofilm resistance to antimicrobial compounds in the plant-pathogenic bacterium Xylella fastidiosa reveals evidence of persister cells
  Muranaka, Journal of bacteriology 2012
  • “...was the result of an assay with four genes (XF2421, XF1353, XF0656, and XF0204) whose transcript levels remained constant during all of the stress conditions...”

NGO1493 putative ribosomal protein S20 from Neisseria gonorrhoeae FA 1090
53% identity, 99% coverage

• RpoH mediates the expression of some, but not all, genes induced in Neisseria gonorrhoeae adherent to epithelial cells
  Du, Infection and immunity 2006
  • “...NGO1988 NGO0234 NGO0721 NGO1366 NGO1291 NGO0199 NGO1515 NGO1493 NGO1439 NGO0989 NGO1831 NGO1841 NGO1668 NGO0637 NGO1773 NGO2180 NGO0962 NGO5041 NGO1587 NGO0276...”

BU151 30S ribosomal protein S20 from Buchnera aphidicola str. APS (Acyrthosiphon pisum)
54% identity, 93% coverage

• Remaining flexible in old alliances: functional plasticity in constrained mutualisms
  Wernegreen, DNA and cell biology 2009
  • “...BU525 BUsg506 Bbp468 rpsT b0023 Bpen120 Bfl116 WGLp296 BU151 BUsg144 Bbp140 rseP (yaeL) b0176 Bpen286 Bfl278 WGLp385 - - - Cleaves RseA, thereby activating...”

BP2773 30S ribosomal protein S20 from Bordetella pertussis Tohama I
NP_881377 30s ribosomal protein s20 from Bordetella pertussis Tohama I
52% identity, 99% coverage

• A gel-free proteomic-based method for the characterization of Bordetella pertussis clinical isolates
  Williamson, Journal of microbiological methods 2012
  • “...CM 24 (3) 24 (3) 19 (2) Energy metabolism 30s ribosomal protein S20 ^ NP_881377 BP2773 rspT 90 U 14 (2) 13 (1) 14 (2) Translation Putative membrane-bound transglycosylase ^ NP_881812 BP3268 Pu 47 OM 4 (1) 14 (4) 16 (4) Membrane biogenesis Putative transglycosylase ^...”
• A gel-free proteomic-based method for the characterization of Bordetella pertussis clinical isolates
  Williamson, Journal of microbiological methods 2012
  • “...23 CM 24 (3) 24 (3) 19 (2) Energy metabolism 30s ribosomal protein S20 ^ NP_881377 BP2773 rspT 90 U 14 (2) 13 (1) 14 (2) Translation Putative membrane-bound transglycosylase ^ NP_881812 BP3268 Pu 47 OM 4 (1) 14 (4) 16 (4) Membrane biogenesis Putative transglycosylase...”

OFBG_01579 30S ribosomal protein S20 from Oxalobacter formigenes OXCC13
57% identity, 88% coverage

• Proteome Dynamics of the Specialist Oxalate Degrader Oxalobacter formigenes
  Ellis, Journal of proteomics & bioinformatics 2016
  • “...HOxBLS genome (OFAG_01539). By comparing the location of OFAG_01539 with the OxCC13 genome, we identified OFBG_01579 (predicted protein) as the probable S20/L26 ribosomal protein encoding gene. Both genes are 273 nucleotides. DNA sequence alignment of HOxBLS gene OFAG_01539 with OxCC13 gene OFBG_01579 showed an 84% similarity,...”

G372_RS0102750 30S ribosomal protein S20 from Thioalkalivibrio thiocyanoxidans ARh2
51% identity, 97% coverage

• Analysis of the Genes Involved in Thiocyanate Oxidation during Growth in Continuous Culture of the Haloalkaliphilic Sulfur-Oxidizing Bacterium Thioalkalivibrio thiocyanoxidans ARh 2^T Using Transcriptomics
  Berben, mSystems 2017
  • “...G372_RS0101520 1.59 3.63E-12 Hypothetical protein G372_RS0102735 1.73 2.80E-10 Sulfite oxidase G372_RS0102740 1.52 6.26E-12 6,7-Dimethyl-8-ribityllumazine synthase G372_RS0102750 1.70 7.83E-17 30S ribosomal protein S20 G372_RS0102895 1.93 1.20E-14 Hypothetical protein G372_RS0102900 1.77 1.47E-10 Adenylyl-sulfate reductase subunit alpha G372_RS0102905 1.65 3.73E-7 Adenylyl-sulfate reductase subunit beta G372_RS0103005 1.86 3.75E-11 30S ribosomal...”

OFAG_01539 30S ribosomal protein S20 from Oxalobacter paraformigenes
56% identity, 88% coverage

• Proteome Dynamics of the Specialist Oxalate Degrader Oxalobacter formigenes
  Ellis, Journal of proteomics & bioinformatics 2016
  • “...not annotated in the O. formigenes OxCC13 genome; however, is present in the HOxBLS genome (OFAG_01539). By comparing the location of OFAG_01539 with the OxCC13 genome, we identified OFBG_01579 (predicted protein) as the probable S20/L26 ribosomal protein encoding gene. Both genes are 273 nucleotides. DNA sequence...”

A6T4F8 Small ribosomal subunit protein bS20 from Klebsiella pneumoniae subsp. pneumoniae (strain ATCC 700721 / MGH 78578)
65% identity, 70% coverage

• Zinc limitation in Klebsiella pneumoniae profiled by quantitative proteomics influences transcriptional regulation and cation transporter-associated capsule production
  Sukumaran, BMC microbiology 2021
  • “...name Protein name A6T4Q9 -5.672 lpdA Dihydrolipoyl dehydrogenase A6T4Q7 -5.271 aceE Pyruvate dehydrogenase E1 component A6T4F8 -5.135 rpsT 30S ribosomal protein S20 A6TGT4 -5.043 pgi Glucose-6-phosphate isomerase A6T6Q8 -4.366 ompX Outer membrane protein X A6T9L3 -4.238 adhP Alcohol dehydrogenase A6TG36 -4.018 atpD ATP synthase subunit beta...”

Bfl116 30S ribosomal protein S20 from Candidatus Blochmannia floridanus
Q7VQL2 Small ribosomal subunit protein bS20 from Blochmanniella floridana
49% identity, 98% coverage

• Remaining flexible in old alliances: functional plasticity in constrained mutualisms
  Wernegreen, DNA and cell biology 2009
  • “...Bpen197 Bfl190 WGLp542 BU525 BUsg506 Bbp468 rpsT b0023 Bpen120 Bfl116 WGLp296 BU151 BUsg144 Bbp140 rseP (yaeL) b0176 Bpen286 Bfl278 WGLp385 - - - Cleaves RseA,...”
• Sample Stability and Protein Composition of Saliva: Implications for Its Use as a Diagnostic Fluid.
  Esser, Biomarker insights 2008
  • “...33872 95% confidence proteins 14-3-3 protein sigma P31947 Signalling 27774 30S ribosomal protein S20 # Q7VQL2 Micro organism 10264 50S ribosomal protein L5 # Q8CRH2 Micro organism 20236 Acetyl-CoA acetyltransferase # P45359 Energy/metabolism 41241 Alanyl-tRNA synthetase # Q971J4 Micro organism 103675 Alpha-2-macroglobulin precursor P01023 Protein Degradation/Inhibitor...”

Dshi_3371 ribosomal protein S20 from Dinoroseobacter shibae DFL 12
48% identity, 98% coverage

• A dual-species co-cultivation system to study the interactions between Roseobacters and dinoflagellates
  Wang, Frontiers in microbiology 2014
  • “...carrier protein 282 0.7 91 0.5 Dshi_1968 Pyruvate dehydrogenase E1 component 263 0.6 180 0.9 Dshi_3371 Ribosomal protein S20 172 0.4 126 0.6 Dshi_3556 Sodium/solute symporter family protein 242 0.6 111 0.6 Since the selection of fragments for sequencing is a random process, we considered the...”

Rmet_2904 30S ribosomal protein S20 from Cupriavidus metallidurans CH34
50% identity, 98% coverage

• Importance of RpoD- and Non-RpoD-Dependent Expression of Horizontally Acquired Genes in Cupriavidus metallidurans
  Große, Microbiology spectrum 2022
  • “...rpmE 12.2 7 35 TTGATTCGTC 13 TCTATAATGT Rmet_2870 rpmB 14.2 38 36 TTGCCTGTCC 14 TGTATAATCG Rmet_2904 rpsT 14.4 33 35 TTGCAGTTTT 14 TTTATAATCA Rmet_3106 rplU 12.6 1,622 39 TGGCGCCGTG 15 GATAAAGTGG Rmet_3291 rpoA 4.9 60 34 TTGCAAGTCC 14 GCTATAATCC Rmet_3307 rplN 11.6 526 34 TTGCCCTTTC 13...”

BPSL0871 putative 30S ribosomal protein S20 from Burkholderia pseudomallei K96243
BTH_I0735 ribosomal protein S20 from Burkholderia thailandensis E264
49% identity, 93% coverage

• Unraveling the role of toxin-antitoxin systems in <i>Burkholderia pseudomallei</i>: exploring bacterial pathogenesis and interactions within the HigBA families
  Chapartegui-González, Microbiology spectrum 2024
  • “...genes that encode for proteins related to ribosomal functions (BPSL1458, BPSL1460, BPSL1461, BPSL1491, BPSL0915, BPSL0916, BPSL0871, BPSL1355, BPSL1206, BPSL1511, BPSL0520, and BPSL0075a) were identified. When the different strains were exposed to ciprofloxacin, the double mutants lacking the whole TA system exhibited reduced survival compared with the...”
• Gene and protein expression in response to different growth temperatures and oxygen availability in Burkholderia thailandensis
  Peano, PloS one 2014
  • “...and RNA polymerase (54) BTH_I0473 ( rplY ) ribosomal protein L25 6.50 2.7 150 All BTH_I0735 ( rpsT ) S20 4.59 2.2 All [33] BTH_I0779 ( rpmG ) L33 3.73 1.9 All rpmG rpmB BTH_I0780 ( rpmB ) L28 3.73 1.9 150 All rpmG rpmB BTH_I1055...”

bglu_1g29160 30S ribosomal protein S20 from Burkholderia glumae BGR1
49% identity, 95% coverage

• RNAseq-based Transcriptome Analysis of Burkholderia glumae Quorum Sensing
  Kim, The plant pathology journal 2013
  • “...0.5 1.5 1.6 bglu_1g28680 rpmB 0.7 0.6 1. 1 bglu_1g28690 rpmG 0.5 0.4 1.5 1.1 bglu_1g29160 rpsT 0.9 0.8 1.8 1.4 bglu_1g31330 rplY 1.1 0.7 0.8 0.9 bglu_2g15900 rpsU 0.5 0 1.5 1.1 1 log 2 (R1/S2) = log 2 (BGR1/BGS2) 2 log 2 (R1/S9) =...”

Pden_4514 ribosomal protein S20 from Paracoccus denitrificans PD1222
49% identity, 97% coverage

• Paracoccus denitrificans PD1222 utilizes hypotaurine via transamination followed by spontaneous desulfination to yield acetaldehyde and, finally, acetate for growth
  Felux, Journal of bacteriology 2013
  • “...Pden_2832) or chromosome 2 (locus tags Pden_2833 to Pden_4514) of P. denitrificans PD1222. ELSD (gradient-HILIC-UV-ELSD). Alanine, HT, NADH, and NAD eluted at...”

BA_4994 Ribosomal_S20p, Ribosomal protein S20 from Bacillus anthracis str. A2012
BC4320, NP_834032 SSU ribosomal protein S20P from Bacillus cereus ATCC 14579
BC_4320 30S ribosomal protein S20 from Bacillus cereus ATCC 14579
51% identity, 99% coverage

• c-di-AMP accumulation impairs toxin expression of Bacillus anthracis by down-regulating potassium importers
  Hu, Microbiology spectrum 2024
  • “...receptors. Cold c-di-AMP/ATP was added as a competitor where indicated. KtrC (BA_4191), KhtT (BA_5287), KhtT-2 (BA_4994), and YjbQ (BA_0699) are RCK domain-containing proteins. Prov2 (BA_2786), YkuL (BA_4196), YrkA (BA_3422), AcuB (BA_4917), CcpN (BA_4521), YtoI (BA_4858), CbpA-1 (BA_2601), and CbpA-2 (BA_1348) are CBS domain-containing proteins. In total,...”
  • “...+ transporter RCK_C pET28a- khtT BA_5287 a K + /H + antiporter RCK_C pET28a- khtT-2 BA_4994 a K + /H + antiporter RCK_C pET28a- yjbQ BA_0699 a Potassium exporter RCK_C pET28a- yugo BA_5182 Unknown function RCK_C pET28a- kdpD BA_0742 a Putative sensor protein pET28a- prov2 BA_2786...”
• SigB modulates expression of novel SigB regulon members via Bc1009 in non-stressed and heat-stressed cells revealing its alternative roles in Bacillus cereus
  Yeak, BMC microbiology 2023
  • “...Annotation wt 42C/ sigB 42C log2 FC wt 42C/ bc1009 42C log2 FC COG 1 BC4320 RpsT SSU ribosomal protein, translation -6.2 J 2 BC1699 BC1699 ECF-type sigma factor negative effector -4.9 S 3 BC2026 BC2026 Oligopeptide-binding protein oppA -4.8 E 4 BC0450 YfkJ Protein tyrosine...”
• Proteomic evidences for rex regulation of metabolism in toxin-producing Bacillus cereus ATCC 14579
  Laouami, PloS one 2014
  • “...BC_0120 NP_830001 50 S ribosomal protein L7/L12 N N 1,7 0,03 1,1 0,03 RpsT BC_4320 NP_834032 30 S ribosomal protein S20 N N ND ND 2 0,03 RplX BC_0142 NP_830022 50 S ribosomal protein L24 N N 2,2 0,03 0,79 0,154 RpmD BC_0149 NP_830029 50 S...”
• Proteomic evidences for rex regulation of metabolism in toxin-producing Bacillus cereus ATCC 14579
  Laouami, PloS one 2014
  • “...RplL BC_0120 NP_830001 50 S ribosomal protein L7/L12 N N 1,7 0,03 1,1 0,03 RpsT BC_4320 NP_834032 30 S ribosomal protein S20 N N ND ND 2 0,03 RplX BC_0142 NP_830022 50 S ribosomal protein L24 N N 2,2 0,03 0,79 0,154 RpmD BC_0149 NP_830029 50...”

BMEI1944 SSU ribosomal protein S20P from Brucella melitensis 16M
BAB1_2186 Ribosomal protein S20 from Brucella melitensis biovar Abortus 2308
48% identity, 98% coverage

• Identification of a Novel Small Non-Coding RNA Modulating the Intracellular Survival of Brucella melitensis
  Wang, Frontiers in microbiology 2015
  • “...gene Predicted length (nt) Probe location a 5 3 1 BSR1944 b AE008917 2004088-2003970 BMEI1945 BMEI1944 119 2100 2 BSR0742 AE008918 781743-781583 BMEII0743 BMEII0742 161 26133 3 BSR0709 b AE008918 750924-750608 BMEII0710 BMEII0709 317 159289 4 BSR0653 b AE008918 684479-683838 BMEII0654 BMEII0653 642 127307 5 BSR1350...”
• Proteomics-based confirmation of protein expression and correction of annotation errors in the Brucella abortus genome
  Lamontagne, BMC genomics 2010
  • “...GrpE BAB1_1070 WrbA BAB1_1559 FbcF BAB1_2176 YaeC/NLPA lipoprotein BAB1_0389 CcoP BAB1_1113 Unknown; conserved BAB1_1641 Unknown BAB1_2186 RpsT; S20 BAB1_0413 AtpB BAB1_1152 PdhA BAB1_1647 FabG domain BAB2_0207 Unknown BAB1_0418 Unknown BAB1_1230 RplQ; L17 BAB1_1693 bZIP BAB2_0243 YedY BAB1_0420 Unknown BAB1_1232 RpsK; S11 BAB1_1728 RpmE; L31 BAB2_0269 RpsU;...”

BCAL2765 30S ribosomal protein S20 from Burkholderia cenocepacia J2315
45% identity, 96% coverage

• Identification of small RNAs abundant in Burkholderia cenocepacia biofilms reveal putative regulators with a potential role in carbon and iron metabolism
  Sass, Scientific reports 2017
  • “...e.g. ribonuclease E 34 (BCAL2888), a proline-betaine transporter 35 (BCAL1252), ribosomal proteins 36 (BCAL0115, BCAL2091, BCAL2765, BCAL2714, BCAL3348), carA 37 (BCAL1260) and tRNA-synthetases 36 (BCAL3373, BCAL3436). Attenuation, observed for many short 5UTRs, is indicative of a cis-regulatory function. Overall, 5UTRs of B. cenocepacia are an abundant...”
• Whole-Genome Sequencing of Three Clonal Clinical Isolates of B. cenocepacia from a Patient with Cystic Fibrosis
  Miller, PloS one 2015
  • “...- 2873956 BCAL2615 putative exported outer membrane porin protein G G G A S 3037135 BCAL2765 rpsT 30S ribosomal protein S20 C C C T S 3043868 BCAL2772 putative AMP-binding enzyme T T T G V494G NS Neutral -1.75 3201111 BCAL2920 subfamily M48A metalopeptidase T T...”

RHE_RS01805 30S ribosomal protein S20 from Rhizobium etli CFN 42
44% identity, 93% coverage

• Rhizobium etli CFN42 proteomes showed isoenzymes in free-living and symbiosis with a different transcriptional regulation inferred from a transcriptional regulatory network
  Taboada-Castro, Frontiers in microbiology 2022
  • “...transport system substrate-binding protein K10439 Bacteroid RHE_RS29865 rbsB; ribose transport system substrate-binding protein K02968 MM RHE_RS01805 RP-S20, rpsT; small subunit ribosomal protein S20 K02968 Bacteroid RHE_RS01805 RP-S20, rpsT; small subunit ribosomal protein S20 K01609 MM RHE_RS11125 trpC; indole-3-glycerol phosphate synthase [EC:4.1.1.48] K01609 Bacteroid RHE_RS11125 trpC; indole-3-glycerol...”

FN1879 SSU ribosomal protein S20P from Fusobacterium nucleatum subsp. nucleatum ATCC 25586
41% identity, 96% coverage

• Proteomics of Fusobacterium nucleatum within a model developing oral microbial community
  Hendrickson, MicrobiologyOpen 2014
  • “...FN1635, FN1637, FN1638, FN1639, FN1640, FN1641, FN1642, FN1643, FN1644, FN1645, FN1646, FN1656, FN1657, FN1781, FN1828, FN1879, FN1979, FN2037, FN2038, FN2039, FN2040. 3 Covers FN0040, FN0054, FN0067, FN0069, FN0070, FN0110, FN0298, FN0299, FN0405, FN0466, FN0506, FN0611, FN0697, FN0753, FN0754, FN0755, FN1268, FN1340, FN1489, FN1517, FN1579, FN1597, FN1658,...”

ZMO1358 30S ribosomal protein S20 from Zymomonas mobilis subsp. mobilis ZM4
43% identity, 99% coverage

• Identification and Characterization of Genes Related to Ampicillin Antibiotic Resistance in Zymomonas mobilis
  Geng, Antibiotics (Basel, Switzerland) 2022
  • “...sequences containing a 5NTTN3 PAM for six genes of ZMO0103 , ZMO0893 , ZMO1094 , ZMO1358 , ZMO1866, and ZMO1967 . The oligonucleotides of spacers were ordered from TsingKe Biotechnology Co., Ltd. (Beijing, China). CRISPRCas12aediting plasmids were constructed following the previous description [ 25 ]. The...”

Swit_4886 30S ribosomal protein S20 from Sphingomonas wittichii RW1
50% identity, 99% coverage

• Sphingomonas wittichii Strain RW1 Genome-Wide Gene Expression Shifts in Response to Dioxins and Clay
  Chai, PloS one 2016
  • “...at Arizona State University. Genome sequences of RW1, chromosomal (NC_00911, open reading frames Swit_0001 to Swit_4886), plasmid pSWIT01 (NC_009507, Swit_5113 to Swit_5400) and plasmid pSWIT02 (NC_00908, Swit_4887 to Swit_5112), and annotations were downloaded from the Joint Genome Institute (JGI, http://genome.jgi-psf.org/sphwi/sphwi.home.html ). Pathway information for RW1 was...”

RLV_7380 30S ribosomal protein S20 from Rhizobium leguminosarum bv. viciae
43% identity, 93% coverage

• Genomic Diversity in the Endosymbiotic Bacterium Rhizobium leguminosarum
  Sánchez-Cañizares, Genes 2018
  • “...pRL132504 88.80 37.39 Rlt WSM2304 pRLG201 84.22 36.78 Rlt WSM2304 pRLG204 86.98 33.77 Chr RLV_2742- RLV_7380 Rlv 3841 chr 93.08 81.83 Rlt WSM1325 chr 92.79 82.72 Rlt WSM2304 chr 88.85 73.06 ORF: Open Reading Frame....”

8crxT / Q6A9B3 8crxT (see paper)
46% identity, 97% coverage

• Ligand: rna (8crxT)

RB7022 probable 30S ribosomal protein S20 from Pirellula sp. 1
RB7022 30S ribosomal protein S20 from Rhodopirellula baltica SH 1
46% identity, 92% coverage

• Life cycle analysis of the model organism Rhodopirellula baltica SH 1(T) by transcriptome studies
  Wecker, Microbial biotechnology 2010
  • “...the expression level of genes belonging to the ribosomal machinery (RB12197, RB2543, RB264, RB5801, RB5804, RB7022, RB7818, RB8253, RB8725 and RB9304), transcription regulation (RB10339, RB10458, RB11223, RB12372 and RB1392) and DNA replication and recombination (RB11863 and RB3281) in the late stationary phase, probably due to reduced...”

RS20_BACSU / P21477 Small ribosomal subunit protein bS20; 30S ribosomal protein S20; BS20 from Bacillus subtilis (strain 168) (see paper)
BSU25550 30S ribosomal protein S20 from Bacillus subtilis subsp. subtilis str. 168
41% identity, 98% coverage

• function: Binds directly to 16S ribosomal RNA
  subunit: Part of the 30S ribosomal subunit.
• The Blueprint of a Minimal Cell: MiniBacillus
  Reuß, Microbiology and molecular biology reviews : MMBR 2016
  • “...BSU01420 BSU01100 BSU01410 BSU01290 BSU16680 BSU15990 BSU01250 BSU40890 BSU01200 BSU25550 BSU25410 No Yes Yes Yes Yes Yes No Yes No Yes Yes Yes No Yes Yes Yes...”
• Secondary structural entropy in RNA switch (Riboswitch) identification
  Manzourolajdad, BMC bioinformatics 2015
  • “...nt 2625315 2625514 forward BSU25420 yqeW -3576 -54.30 - 0.4850 124.8850021 - 0.3550 10402 rpsT BSU25550 0.8240758777 200 nt 4007404 4007603 forward BSU39020 yxjA -360 -48.97 - 0.4150 124.6660004 - 0.3950 2902 citH BSU39060 0.8239642382 200 nt 2376722 2376921 forward BSU22510 ypjC -15121 -44.40 - 0.3450...”
• Proteomics analyses of Bacillus subtilis after treatment with plumbagin, a plant-derived naphthoquinone
  Reddy, Omics : a journal of integrative biology 2015
  • “...protein S16 OS P21476 30S ribosomal protein S19 OS P21477 30S ribosomal protein S20 OS P21470 30S ribosomal protein S9 OS Q06796 50S ribosomal protein L11 OS...”

NCgl2261 30S ribosomal protein S20 from Corynebacterium glutamicum ATCC 13032
cg2573 30S ribosomal protein S20 from Corynebacterium glutamicum ATCC 13032
47% identity, 99% coverage

• Bacterial EndoMS/NucS acts as a clamp-mediated mismatch endonuclease to prevent asymmetric accumulation of replication errors
  Takemoto, Nucleic acids research 2018
  • “...) were not found in C. glutamicum . The C. glutamicum homologues of Rv2412 ( NCgl2261 ) and Rv2738c ( NCgl1806 ) were annotated as ribosomal protein and phage integrase, respectively, and were not analyzed further. We attempted to obtain a C. glutamicum in-frame deletion mutant...”
• Transcriptome analysis of Corynebacterium glutamicum in the process of recombinant protein expression in bioreactors
  Sun, PloS one 2017
  • “...were 10 genes that were hypothetical proteins. Eleven genes encoded ribosomal proteins (NCgl1304, NCgl0538, NCgl1901, NCgl2261, NCgl0518, NCgl0515, NCgl0495, NCgl0487, NCgl0833, NCgl1325, NCgl0488); however, most of them were down-regulated under C . glutamicum EGFP, indicating that the translation process was suppressed with EGFP expression. There were...”
  • “...transport should be considered. First, the genes related to ribosomal protein were mostly down-regulated; however, NCgl2261 encoding the 30S ribosomal protein S20 was up-regulated with EGFP expression. The cause may be that the down-regulation of ribosomal protein could save more ATP and substance. Second, the three...”
• Adaptation of Corynebacterium glutamicum to ammonium limitation: a global analysis using transcriptome and proteome techniques
  Silberbach, Applied and environmental microbiology 2005
  • “...and turnover NCgl0477 NCgl0515 NCgl0516 NCgl0556 NCgl0557 NCgl2261 NCgl1075 NCgl1844 NCgl2520 NCgl2682 cg0582 cg0628 cg0629 cg0673 cg0674 cg2573 cg1271 cg2102...”
• Functional genomics of pH homeostasis in Corynebacterium glutamicum revealed novel links between pH response, oxidative stress, iron homeostasis and methionine synthesis
  Follmann, BMC genomics 2009
  • “...0 -2.73 -2.19 - 4.9 2.4 - -0.3 - - - - RamA, RamB 78 cg2573 rpsT 30S ribosomal protein S20 0 -1.33 -0.56 2.8 3.3 2.1 2.7 2.7 3.5 1.6 1.4 1.2 79 cg2603 ndk Nucleoside diphosphate kinase 0 -1.19 -0.20 2.8 3.3 3.2 -...”
• Global gene expression during stringent response in Corynebacterium glutamicum in presence and absence of the rel gene encoding (p)ppGpp synthase
  Brockmann-Gretza, BMC genomics 2006
  • “...rpsO 30S ribosomal protein S15 J cg2253 0.53 0.49 rpsP 30S ribosomal protein S16 J cg2573 0.41 0.30 rpsT 30S ribosomal protein S20 J cg2595 0.65 0.64 rplU 50S ribosomal protein L21 J cg3140 0.13 0.35 tagA1 DNA-3-methyladenine glycosylase I L cg3141 0.22 0.46 hmp NO-detoxification...”
• Adaptation of Corynebacterium glutamicum to ammonium limitation: a global analysis using transcriptome and proteome techniques
  Silberbach, Applied and environmental microbiology 2005
  • “...NCgl1075 NCgl1844 NCgl2520 NCgl2682 cg0582 cg0628 cg0629 cg0673 cg0674 cg2573 cg1271 cg2102 cg2890 cg3079 rpsG rpsH rplF rplM rpsI rpsT sigE sigB clpB 1.76 2.09...”

Atu0323 30S ribosomal protein S20 from Agrobacterium tumefaciens str. C58 (Cereon)
41% identity, 98% coverage

• A central role for the transcriptional regulator VtlR in small RNA-mediated gene regulation in Agrobacterium tumefaciens
  Budnick, Scientific reports 2020
  • “...Table S3 ), including promoters from the following genes: atu0036 , atu0055 , atu0157 , atu0323 , atu0463 , atu2708 , atu3939 , atu4669 , atu5116 , atu5119 , atu5121 , atu5161 , atu5118 , atu0484 , atu0828 , atu1296 , atu2187 , atu2350 , atu2384...”
• Deep sequencing uncovers numerous small RNAs on all four replicons of the plant pathogen Agrobacterium tumefaciens
  Wilms, RNA biology 2012
  • “...70 C2 112675 112536 atu0109 / atu8081 - 139, 98 140, 95 C3 317175 317330 atu0323 / atu0324 - 155 170, 70 C4 998103 998034 atu1000 / atu1001 - 69 50 C5 1275442 1275296 - atu1287 146 140 C6 1288585 1288698 atu1298 / atu1299 - 113...”

8buut / P21477 8buut (see paper)
40% identity, 98% coverage

• Ligand: rna (8buut)

MSMEG_4571 ribosomal protein S20 from Mycobacterium smegmatis str. MC2 155
MSMEG_4571 30S ribosomal protein S20 from Mycolicibacterium smegmatis MC2 155
42% identity, 100% 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
  • “..., msmeg_3791-3793, msmeg_4624-4625 as well as isolated ORFs msmeg_1339, msmeg_1346, msmeg_1428, msmeg_2435, msmeg_2440, msmeg_2541, msmeg_2564, msmeg_4571, msmeg_4580, msmeg_4951, msmeg_5222, msmeg_5431, msmeg_5489, msmeg_6894, msmeg_6897 and msmeg_6946 . MnoRS weakly influences utilization of sugars as carbon sources and does not affect nitrogen metabolism Next, we ask the question...”
• Elucidating the role of c-di-AMP in Mycobacterium smegmatis: Phenotypic characterization and functional analysis
  Chaudhary, Heliyon 2023
  • “...protein L31 1.73 0.034 3 rpmH (MSMEG_6946) 50S ribosomal protein L34 1.13 0.031 4 rpsT (MSMEG_4571) 30S ribosomal protein S20 1.60 0.023 5 rplL (MSMEG_1365) 50S ribosomal protein L7/L12 2.43 0.027 6 rplI (MSMEG_6894) 50S ribosomal protein L9 1.94 0.039 7 rpsP (MSMEG_2435) 30S ribosomal protein...”
• Identification of Mycobacterial Genes Involved in Antibiotic Sensitivity: Implications for the Treatment of Tuberculosis with β-Lactam-Containing Regimens
  Viswanathan, Antimicrobial agents and chemotherapy 2017
  • “...MSMEG_0035 1,464 194 fhaA FHA domain protein TR58 MSMEG_4571 261 88 rpsT 30S ribosomal protein S20 TR62 MSMEG_6939 972 650 parA Chromosome partitioning protein...”
• Gene Expression, Bacteria Viability and Survivability Following Spray Drying of Mycobacterium smegmatis
  Lauten, Materials (Basel, Switzerland) 2010
  • “...S18 rpsR 1.4 12.2 0.001 88% MSMEG_1440 ribosomal protein S19 rpsS 1.4 12.1 0.001 97% MSMEG_4571 ribosomal protein S20 rpsT 0.5 12.1 0.033 4% materials-03-02684-t003_Table 3 Appendix Table 2 Select up-regulated operons and clusters in log phase over stationary phase (non-spray dried log versus stationary comparision)....”

ruthe_02250 30S ribosomal protein S20 from Rubellimicrobium thermophilum DSM 16684
43% identity, 83% coverage

• Genome sequence of the reddish-pigmented Rubellimicrobium thermophilum type strain (DSM 16684(T)), a member of the Roseobacter clade
  Fiebig, Standards in genomic sciences 2013
  • “...to 03172). Additionally, several gene sequences associated with CRISPRs (ruthe_02227 to 02230, ruthe_02232 to 02234, ruthe_02250, ruthe_02251, ruthe_02253 and ruthe_02255), cytochrome c oxidase activity (ruthe_00413 to 00417), cytochrome cbb3 oxidase activity (ruthe_01647 to 01654) as well as cytochrome bd-I ubiquinol oxidase activity (ruthe_01776, ruthe_01777) were found....”

8fmwT / P49394 8fmwT (see paper)
BB0233 30S ribosomal protein S20 from Borrelia burgdorferi B31
46% identity, 92% coverage

• Ligand: rna (8fmwT)
• Stage-specific global alterations in the transcriptomes of Lyme disease spirochetes during tick feeding and following mammalian host adaptation
  Iyer, Molecular microbiology 2015
  • “...bb0396 ribosomal protein L33 24 35 23 22 bb0232 hbbU protein 25 25 62 38 bb0233 ribosomal protein S20 26 31 344 70 bb0423 hypothetical protein 27 22 7 9 bb0293 flagellar basal-body rod protein, FlgC 28 108 123 39 bb0355 CarD-like transcriptional regulator, LtpA 29...”
• Profiling of temperature-induced changes in Borrelia burgdorferi gene expression by using whole genome arrays
  Ojaimi, Infection and immunity 2003
  • “...transcript level 35 23 BB0440 BBA59 BB0049 BB0804 BB0233 BB0162 BB0500 BBA62 BB0232 BB0294 BB0559 BBA15 BB0300 BB0778 BBB19 BB0480 BB0486 BB0704 BB0365 BBA32...”
  • “...gene) Relative transcript level 23 35 BB0440 BBA59 BB0233 BB0049 BB0559 BB0804 BBA62 BB0300 BB0294 BB0500 BBA15 BB0232 BB0778 BB0047 BB0162 BB0486 BB0355 BBA16...”

Q8A276 Small ribosomal subunit protein bS20 from Bacteroides thetaiotaomicron (strain ATCC 29148 / DSM 2079 / JCM 5827 / CCUG 10774 / NCTC 10582 / VPI-5482 / E50)
42% identity, 100% coverage

• Comparative Proteomic Analysis of Fucosylated Glycoproteins Produced by Bacteroides thetaiotaomicron Under Different Polysaccharide Nutrition Conditions
  Tian, Frontiers in microbiology 2022
  • “...0.33 4.10 0.08 Fucoidan Vs. Glc Q8A5U4 Putative oxidoreductase BT_2144 F unique 1.06 F unique Q8A276 30S ribosomal protein S20 rpsT F unique 0.86 F unique Q8A3F4 T5orf172 domain-containing protein BT_3000 F unique 0.63 F unique Q8A7N3 DUF4465 domain-containing protein BT_1491 F unique 0.57 F unique...”

MAV_1770 ribosomal protein S20 from Mycobacterium avium 104
43% identity, 100% coverage

• Surface proteome of "Mycobacterium avium subsp. hominissuis" during the early stages of macrophage infection
  McNamara, Infection and immunity 2012
  • “...1 6 2 8 1 5 2 1 2 2 2 2 2 MAV_5147 MAV_1525 MAV_1527 MAV_4462 MAV_1770 MAV_3744 MAV_3759 MAV_1729 MAV_4503 6 7 10 5 4 2 1 2 3 5 9 11 2 3 1 1 1 2 3 6 10 4 3 1 2...”
  • “...surface, most notably multiple ribosomal proteins (MAV_4462, MAV_1770, MAV_3744, MAV_3759, and MAV_1729) and elongation factor Tu (tuf, MAV_4489). The question...”

SMc01152 30S RIBOSOMAL PROTEIN S20 from Sinorhizobium meliloti 1021
42% identity, 98% coverage

• Antimicrobial nodule-specific cysteine-rich peptides induce membrane depolarization-associated changes in the transcriptome of Sinorhizobium meliloti
  Tiricz, Applied and environmental microbiology 2013
  • “...SMc00364 SMc00485 SMc00565 SMc00567 SMc00568 SMc00704 SMc01152 SMc01283 SMc01286 SMc01287 SMc01290 SMc01291 SMc01292 SMc01293 SMc01294 SMc01295 SMc01296...”

6dzi7 / A0R102 6dzi7 (see paper)
41% identity, 99% coverage

• Ligand: rna (6dzi7)

SCO2563 30s ribosomal protein S20 from Streptomyces coelicolor A3(2)
44% identity, 98% coverage

• Comparative genomics of Streptomyces avermitilis, Streptomyces cattleya, Streptomyces maritimus and Kitasatospora aureofaciens using a Streptomyces coelicolor microarray system
  Hsiao, Antonie van Leeuwenhoek 2008
  • “...protein L35 0.23 0.41 0.49 0.51 SCO1998 30S ribosomal protein S1 1.39 0.77 0.99 0.91 SCO2563 30s ribosomal protein S20 0.34 0.34 0.77 0.33 SCO2596 50S ribosomal protein L27 1.01 0.59 0.08 0.82 SCO2597 ribosomal protein L21 0.27 0.08 0.64 0.18 SCO3124 ribosomal L25p family protein...”

RS20_RHOPA / Q6N0C7 Small ribosomal subunit protein bS20; 30S ribosomal protein S20; RRP-S20 from Rhodopseudomonas palustris (strain ATCC BAA-98 / CGA009) (see paper)
RPA4836 30S ribosomal protein S20 from Rhodopseudomonas palustris CGA009
42% identity, 98% coverage

• function: Binds directly to 16S ribosomal RNA.
• ATP Is a Major Determinant of Phototrophic Bacterial Longevity in Growth Arrest
  Yin, mBio 2023
  • “...RPA3077, RPA3078, RPA3227, RPA3228, RPA3233, RPA3236, RPA3237, RPA3241, RPA3244, RPA3246, RPA3251, RPA3254, RPA3255, RPA4005, RPA4176, RPA4836; Photosynthesis gene cluster: RPA1505-RPA1554; ATP synthesis: RPA0175-RPA0179, RPA0843-RPA0847. 10.1128/mbio.03609-22.5 TABLES3 List of genes that are differentially expressed (> = 2-fold change, P <0.05) between the experimental conditions described in each...”

YP_003432481 ribosomal protein S20 from Hydrogenobacter thermophilus TK-6
39% identity, 88% coverage

• Phylogenetic position of aquificales based on the whole genome sequences of six aquificales species
  Oshima, International journal of evolutionary biology 2012
  • “...YP_003433556 UDP-N-acetylglucosamine pyrophosphorylase YP_003431738 putative metalloprotease YP_003431749 diaminopimelate decarboxylase YP_003431809 dihydrodipicolinate reductase YP_003431998 UDP-N-acetylglucosamine 1-carboxyvinyltransferase YP_003432481 ribosomal protein S20 YP_003432953 queuine tRNA-ribosyltransferase YP_003431834 ATP-dependent protease La YP_003431839 tRNA delta(2)-isopentenylpyrophosphate transferase YP_003431873 2-C-methyl-D-erythritol 4-phosphate cytidylyltransferase YP_003431915 ribonuclease III YP_003432036 riboflavin synthase alpha chain YP_003432044 DNA polymerase I...”

DVU1896 ribosomal protein S20 from Desulfovibrio vulgaris Hildenborough
38% identity, 99% coverage

• Antimicrobial Effects of Free Nitrous Acid on Desulfovibrio vulgaris: Implications for Sulfide-Induced Corrosion of Concrete
  Gao, Applied and environmental microbiology 2016
  • “...DVU1302 DVU1327 DVU1298 DVU1326 DVU1316 DVU0839 DVU0874 DVU1896 DVU1309 DVU1328 DVU1320 DVU0956 DVU1299 DVU1317 DVU2925 DVU2926 DVU2924 DVU2518 DVU1313 DVU1310...”
• Temporal transcriptomic analysis as Desulfovibrio vulgaris Hildenborough transitions into stationary phase during electron donor depletion
  Clark, Applied and environmental microbiology 2006
  • “...Berkeley DVU2572 DVU2571 DVU1366 DVU2861 DVU2862 DVU2869 DVU1896 DVU1574 DVU1575 DVU1568 DVU0019 DVU2410 DVU1858 DVU0938 DVUA0037 DVU1035 DVUA0043 DVU2285...”

CKC_RS00375 30S ribosomal protein S20 from Candidatus Liberibacter solanacearum CLso-ZC1
39% identity, 88% coverage

• Interactions "Candidatus Liberibacter solanacearum"-Bactericera cockerelli: Haplotype Effect on Vector Fitness and Gene Expression Analyses
  Yao, Frontiers in cellular and infection microbiology 2016
  • “...system, M subunit 5 CKC_RS00790 Ribonuclease E 5 CKC_RS00820 Glycyl-tRNA synthetase subunit alpha: glyQ 5 CKC_RS00375 30S ribosomal protein S20 5 Evaluation of S4TE-predicted effector gene expression by qPCR To evaluate the S4TE-predicted effectors gene expression of Lso A and Lso B associated with psyllids, primers...”
  • “...use ( CKC_RS00980 , CKC_RS02450 , CKC_RS05560 , CKC_RS01855 , CKC_RS00790 , CKC_RS00820 , and CKC_RS00375 ). To evaluate if recA could be used as a reference gene for RT-qPCR analyses, Lso density and recA expression were compared in different samples. For both sexes, a strong...”

Mb2435 PROBABLE 30S RIBOSOMAL PROTEIN S20 RPST from Mycobacterium bovis AF2122/97
MT2485 30S ribosomal protein S20 from Mycobacterium tuberculosis CDC1551
Rv2412 30S ribosomal protein S20 from Mycobacterium tuberculosis H37Rv
42% identity, 100% coverage

• Integrated computational prediction and experimental validation identifies promiscuous T cell epitopes in the proteome of Mycobacterium bovis
  Farrell, Microbial genomics 2016
  • “...Rv1762c Mb1793c EHLEFMAVGTAVRYTAKPGA Binder clusters 64 111 Rv1833c Mb1864c VMSSPPVQYAILRRNFFVER Binder clusters 64 154 Rv2412 Mb2435 RNKAVKSSLRTAVRAFREAA Binder clusters 64 20 Rv3247c Mb3275c ASSVYAMATLFALDRAGAVH Binder clusters 64 62 Peptides with responder frequencies 60% of the mean value for the positive controls. *Start position is the location...”
• Conserved codon composition of ribosomal protein coding genes in Escherichia coli, Mycobacterium tuberculosis and Saccharomyces cerevisiae: lessons from supervised machine learning in functional genomics
  Lin, Nucleic acids research 2002
  • “...MT2855, MT2977, MT0737, MT2116, MT0061, MT0732, MT2958, MT2485, MT0734, MT3565, MT0746, MT0059, MT0711, MT0743, MT3547 Large subunit 46 RPP0, RPP1A, RPP2A,...”
• Bedquiline Resistance Mutations: Correlations with Drug Exposures and Impact on the Proteome in M. tuberculosis
  Xu, Antimicrobial agents and chemotherapy 2023
  • “...ribosomal protein L36 2.0 2.7 1.9 1.9 Rv3190A Rv3190A Conserved protein 2.0 3.0 2.0 1.9 Rv2412 rpsT 30S ribosomal protein S20 1.9 3.8 2.5 2.8 TABLE 9 Top 10 upregulated proteins with the highest average fold changes in the atpE mutant only (H3), but not in...”
• Metabolic Changes of Mycobacterium tuberculosis during the Anti-Tuberculosis Therapy
  Bespyatykh, Pathogens (Basel, Switzerland) 2020
  • “...abundance of RpsL and seven other ribosome proteins (Rv0055, Rv0714, Rv0720, Rv0722, Rv0979A, Rv1298, and Rv2412) was lower compared to the parental strains. This finding may be related to the fact that ribosomal proteins can be targeted by anti-tuberculosis drugs [ 16 ], and, particularly, by...”
• Bacterial EndoMS/NucS acts as a clamp-mediated mismatch endonuclease to prevent asymmetric accumulation of replication errors
  Takemoto, Nucleic acids research 2018
  • “...and Rv3908 ) were not found in C. glutamicum . The C. glutamicum homologues of Rv2412 ( NCgl2261 ) and Rv2738c ( NCgl1806 ) were annotated as ribosomal protein and phage integrase, respectively, and were not analyzed further. We attempted to obtain a C. glutamicum in-frame...”
• The effect of growth rate on pyrazinamide activity in Mycobacterium tuberculosis - insights for early bactericidal activity?
  Pullan, BMC infectious diseases 2016
  • “...L20 2.99 3.56 Rv0723 P95071 50S ribosomal protein L15 1.44 3.38 tRNA-Trp tRNA-Trp 2.97 3.32 Rv2412 P66505 30S ribosomal protein S20 3.07 3.22 Rv0683 P41194 30S ribosomal protein S7 4.07 3.05 Rv0718 P66625 30S ribosomal protein S8 3.13 3.04 Rv1642 P66271 50S ribosomal protein L35 2.59...”
• Integrated computational prediction and experimental validation identifies promiscuous T cell epitopes in the proteome of Mycobacterium bovis
  Farrell, Microbial genomics 2016
  • “...158 Rv1762c Mb1793c EHLEFMAVGTAVRYTAKPGA Binder clusters 64 111 Rv1833c Mb1864c VMSSPPVQYAILRRNFFVER Binder clusters 64 154 Rv2412 Mb2435 RNKAVKSSLRTAVRAFREAA Binder clusters 64 20 Rv3247c Mb3275c ASSVYAMATLFALDRAGAVH Binder clusters 64 62 Peptides with responder frequencies 60% of the mean value for the positive controls. *Start position is the...”
• Transcriptional profile of Mycobacterium tuberculosis replicating in type II alveolar epithelial cells
  Ryndak, PloS one 2015
  • “...of protein synthesis. Of the 23 genes encoding 30S ribosomal proteins, 5 (Rv0682- rpsL , Rv2412- rpsT , Rv3442c- rpsI , Rv3459c- rpsK , Rv3460c- rpsM ) were upregulated in M . tb replicating in type II AEC ( Table 4 ). In contrast, 13 genes...”
• Osmosensory signaling in Mycobacterium tuberculosis mediated by a eukaryotic-like Ser/Thr protein kinase
  Hatzios, Proceedings of the National Academy of Sciences of the United States of America 2013
  • “...Rv1908c Rv1980c Rv1996 Rv2050 Rv2190c Rv2271 Rv2301 Rv2348c Rv2391 Rv2412 Rv2441c Rv2442c Rv2745c Rv2783c Rv2889c 2.7 2.1 2.1 4.0 2.4 2.6 3.1 3.3 2.7 2.8 2.9...”
• Descriptive proteomic analysis shows protein variability between closely related clinical isolates of Mycobacterium tuberculosis
  Mehaffy, Proteomics 2010
  • “...a Rv2376c cfp2 2.24 0.46 0.52 3 1 8.33 [ 17 , 23 ] 15609549 Rv2412 rpsT 0.64 0.74 0.92 2 2 23.26 [ 25 ] 15609579 a Rv2442c rplU 0.83 0.98 1.19 2 1 18.27 15609599 Rv2462c tig 1.35 1.26 1.11 3 5 16.31 [...”
• More

STER_RS04185 30S ribosomal protein S20 from Streptococcus thermophilus LMD-9
43% identity, 97% coverage

• Cell Proteins Obtained by Peptic Shaving of Two Phenotypically Different Strains of Streptococcus thermophilus as a Source of Anti-Inflammatory Peptides
  Allouche, Nutrients 2022
  • “...92.00 STER_1894|ID:1900557| STER_RS09280 30S ribosomal protein S14 type Z (BS21) 7.07 Cyto 11 82.26 STER_0850|ID:1899831|rpsT| STER_RS04185 30S ribosomal subunit protein S20 8.40 Cyto 10 82.28 10 89.87 STHERMOCNRZ21N_v1_31103|ID:59661243|rplX| Ribosomal protein L24 (BL23) 10.86 Cyto 16 69.61 Carbohydrate metabolism and transport STER_0684|ID:1899266|eno| STER_RS03365 Enolase 46.95 CS/M/Cyto 10...”
  • “...36.33 STER_0568|ID:1899173|rplL| STER_RS02800 50S ribosomal subunit protein L7/L12 12.35 Cyto 8 59.35 11 48.78 STER_0850|ID:1899831|rpsT| STER_RS04185 30S ribosomal subunit protein S20 8.40 Cyto 10 89.87 9 89.87 STER_1905|ID:1900568|rplW| STER_RS09335 50S ribosomal subunit protein L23 10.78 Cyto 8 45.46 STHERMOCNRZ21N_v1_31103|ID:59661243|rplX| Ribosomal protein L24 (BL23) 10.86 Cyto 16...”

PG1723 ribosomal protein S20 from Porphyromonas gingivalis W83
PGN_0394 probable 30S ribosomal protein S20 from Porphyromonas gingivalis ATCC 33277
42% identity, 100% coverage

• Microarray analysis of the transcriptional responses of Porphyromonas gingivalis to polyphosphate
  Moon, BMC microbiology 2014
  • “...ribosomal protein L34 6.80 PG0989 50S ribosomal protein L20 3.43 PG0990 Ribosomal protein L35 1.74 PG1723 Ribosomal protein S20 2.94 PG1758 Ribosomal protein S15 6.23 PG1959 Ribosomal protein L33 2.02 PG1960 Ribosomal protein L28 2.03 PG2117 30S ribosomal protein S16 2.93 PG2140 Ribosomal protein L32 3.40...”
• Synthesis of ppGpp impacts type IX secretion and biofilm matrix formation in Porphyromonas gingivalis
  Kim, NPJ biofilms and microbiomes 2020
  • “...2.61 PGN_0188 rpmF 50S ribosomal protein L32 2.21 PGN_0279 rplY 50S ribosomal protein L25 2.07 PGN_0394 rpsT 30S ribosomal protein S20 2.39 PGN_0426 rpsC 30S ribosomal protein S3 3.20 PGN_0636 rpmE2 50S ribosomal protein L31 4.02 PGN_0637 htrA Heat shock-related protease htrA protein 1.93 PGN_0639 rpsF...”
• Pathway analysis for intracellular Porphyromonas gingivalis using a strain ATCC 33277 specific database
  Hendrickson, BMC microbiology 2009
  • “...as determined using DAVID. Increased (32) Unchanged (19) Decreased Levels (1) PGN_0035 PGN_0167 PGN_0640 PGN_0965 PGN_0394 PGN_0188 PGN_0279 PGN_1572 PGN_1589 PGN_0636 PGN_0639 PGN_1647 PGN_1648 PGN_0641 PGN_0964 PGN_1698 PGN_1844 PGN_1088 PGN_1219 PGN_1651 PGN_1852 PGN_1573 PGN_1575 PGN_1853 PGN_1854 PGN_1588 PGN_1590 PGN_1855 PGN_1861 PGN_1832 PGN_1840 PGN_1863 PGN_1868 PGN_1842 PGN_1843...”

Q71ZJ0 Small ribosomal subunit protein bS20 from Listeria monocytogenes serotype 4b (strain F2365)
lmo1480 ribosomal protein S20 from Listeria monocytogenes EGD-e
47% identity, 97% coverage

• Proteomic Exploration of Listeria monocytogenes for the Purpose of Vaccine Designing Using a Reverse Vaccinology Approach
  Srivastava, International journal of peptide research and therapeutics 2021
  • “...1.611 Non-allergen 126 Q725C0 0.638 Non-allergen 127 Q71ZZ5 0.527 Non-allergen 128 Q71ZG8 0.898 Non-allergen 129 Q71ZJ0 1.318 Non-allergen 130 Q71XH4 1.281 Non-allergen 131 Q71WL5 0.848 Non-allergen 132 Q720A8 0.628 Non-allergen 133 Q721Y1 0.988 Non-allergen 134 Q71YM9 1.733 Non-allergen 135 Q71WG4 2.217 Non-allergen 136 Q71YN4 2.371 Non-allergen...”
• Comparison of Surface Proteomes of Adherence Variants of Listeria Monocytogenes Using LC-MS/MS for Identification of Potential Surface Adhesins
  Tiong, Pathogens (Basel, Switzerland) 2016
  • “...biogenesis GTPase (33) CY CY 1.84 (CY,C,E) CM No No 0 No No <1.8 0.44 lmo1480 (3.7.1) 30S ribosomal protein S20 (9) CY CY 0.33 (E,C,CM) CY No No 0 No No <1.8 0.83 lmo1784 (3.7.1) 50S ribosomal protein L35 (8) CY CY 0.33 (E,C,CM) CY...”
• Microarray-based characterization of the Listeria monocytogenes cold regulon in log- and stationary-phase cells
  Chan, Applied and environmental microbiology 2007
  • “...also found to be upregulated at 4C, including lmo1480, lmo1787, lmo2548, lmo2620, lmo2627, and lmo2856 (see Table S2 in the supplemental material). Operons...”

SM12261_RS04005 30S ribosomal protein S20 from Streptococcus mitis NCTC 12261
SPD_0732 ribosomal protein S20 from Streptococcus pneumoniae D39
41% identity, 97% coverage

• Human Serum Supplementation Promotes Streptococcus mitis Growth and Induces Specific Transcriptomic Responses
  Wei, Microbiology spectrum 2023
  • “...ATP-binding protein SM12261_RS03805 1.70 FtsX-like permease family protein 33 SM12261_RS03935 2.92 DUF1797 family protein 34 SM12261_RS04005 1.66 30S ribosomal protein S20 35 SM12261_RS04335 2.09 Lactoylglutathione lyase 36 SM12261_RS04915 1.72 ABC transporter ATP-binding protein 37 SM12261_RS05070 2.08 4-Oxalocrotonate tautomerase 38 SM12261_RS05140 sdbB 1.82 TlpA family protein disulfide...”
• Autoinducer 2 Signaling via the Phosphotransferase FruA Drives Galactose Utilization by Streptococcus pneumoniae, Resulting in Hypervirulence
  Trappetti, mBio 2017
  • “...system II carrier protein 1.5 2.9 2.3 SPD_0558 prtA Cell wall-associated serine protease PrtA 0.5 SPD_0732 30S ribosomal protein 1.6 SPD_0771 lacR1 Lactose phosphotransferase system repressor 1.9 0.3 0.6 SPD_0772 fruB 1-Phosphofructokinase 1.9 0.3 0.5 SPD_0773 fruA PTS, fructose-specific IIABC components 1.7 0.4 0.7 c SPD_0900...”

AS87_RS07650 30S ribosomal protein S20 from Riemerella anatipestifer Yb2
39% identity, 100% coverage

• Riemerella anatipestifer AS87_RS09170 gene is responsible for biotin synthesis, bacterial morphology and virulence
  Ren, Scientific reports 2018
  • “...0.79 AS87_RS00965 50S ribosomal protein L19 0.75 AS87_RS05265 hypothetical protein 0.67 AS87_RS09430 hypothetical protein 0.61 AS87_RS07650 30S ribosomal protein S20 0.60 AS87_RS00160 monofunctional biosynthetic peptidoglycan transglycosylase 0.54 AS87_RS08680 TonB-dependent receptor 0.51 AS87_RS02480 hypothetical protein 0.50 AS87_RS09175 dethiobiotin synthase 0.50 AS87_RS01370 VIT family protein 0.48 AS87_RS07305 cytochrome...”

CTL0881 SSU ribosomal protein S20P from Chlamydia trachomatis 434/Bu
B0B8J2 Small ribosomal subunit protein bS20 from Chlamydia trachomatis serovar L2 (strain ATCC VR-902B / DSM 19102 / 434/Bu)
40% identity, 74% coverage

• Genomewide Transcriptional Responses of Iron-Starved Chlamydia trachomatis Reveal Prioritization of Metabolic Precursor Synthesis over Protein Translation
  Brinkworth, mSystems 2018
  • “...6.58E3 Hypothetical Hypothetical A0A0H3MK96 infA2 CTL0575 2.29 6.70E6 Translation initiation factor IF-1 Translation A0A0H3MDD9 rpsT CTL0881 2.38 1.13E4 Ribosomal subunit Translation B0B8J2 CTL0335 CTL0335 2.43 0.01 Putative integral membrane protein Hypothetical A0A0H3MCX6 ltuA CTL0631 2.68 3.38E3 Late transcription unit A protein Hypothetical A0A0H3MH76 rpsO CTL0215 2.72...”
  • “...assembly rpsO Decrease CTL0215 S15 Ribosomal protein 16S rRNA Assembly of 30S subunit rpsT Decrease CTL0881 S20 Ribosomal protein 16S rRNA Assembly of 30S subunit rpsK Decrease CTL0770 S11 Ribosomal protein 30S subunit Forms Shine-Dalgarno cleft rplT Decrease CTL0207 L20 Ribosomal protein 23S rRNA Assembly of...”
• Genomewide Transcriptional Responses of Iron-Starved Chlamydia trachomatis Reveal Prioritization of Metabolic Precursor Synthesis over Protein Translation
  Brinkworth, mSystems 2018
  • “...2.29 6.70E6 Translation initiation factor IF-1 Translation A0A0H3MDD9 rpsT CTL0881 2.38 1.13E4 Ribosomal subunit Translation B0B8J2 CTL0335 CTL0335 2.43 0.01 Putative integral membrane protein Hypothetical A0A0H3MCX6 ltuA CTL0631 2.68 3.38E3 Late transcription unit A protein Hypothetical A0A0H3MH76 rpsO CTL0215 2.72 4.14E4 Ribosomal subunit Translation B0B972 ndk...”

F452_RS0103275 30S ribosomal protein S20 from Porphyromonas gulae DSM 15663
41% identity, 100% coverage

• Antibacterial effects of sodium tripolyphosphate against Porphyromonas species associated with periodontitis of companion animals
  Lee, Journal of veterinary science 2019
  • “...+9.92 F452_RS0105705 50S ribosomal protein L19 3.37E-64 +8.81 F452_RS0100530 30S ribosomal protein S21 1.88E-100 +10.72 F452_RS0103275 30S ribosomal protein S20 2.71E-63 +10.28 F452_RS0100215 50S ribosomal protein L27 3.46E-33 +4.18 F452_RS0106830 30S ribosomal protein S15 1.30E-41 +6.20 F452_RS0103440 50S ribosomal protein L34 4.64E-96 +14.01 F452_RS0103375 50S ribosomal...”

SSA_1032 30S ribosomal protein subunit S20, putative from Streptococcus sanguinis SK36
41% identity, 97% coverage

• Involvement of signal peptidase I in Streptococcus sanguinis biofilm formation
  Aynapudi, Microbiology (Reading, England) 2017
  • “...0 Helicase No SSA_1224 0.594 2.72E-09 Hypothetical protein No SSA_0670 0.595 1.42E-19 Hypothetical protein No SSA_1032 0.638 4.68E-12 30S ribosomal protein S20 No SSA_2142 0.649 1.09E-18 Argininosuccinate synthase No SSA_2141 0.657 3.25E-11 Argininosuccinate lyase No SSA_1098 0.658 1.32E-08 Formate/nitrate transporter No SSA_2206 1.502 7.86E-06 Hypothetical protein...”
  • “...Tu No SSA_0683 2.57 91.7 DNA-binding protein HU No SSA_0141 2.72 5.57 Copper chaperone No SSA_1032 2.85 7.03 30S ribosomal protein S20 No SSA_0098 3.04 5.18 HAD superfamily hydrolase No SSA_0130 3.2 30.68 30S ribosomal protein S13 No SSA_0112 3.3 24.53 50S ribosomal protein L22 No...”

8uu4t / A0A660JML5 8uu4t (see paper)
47% identity, 94% coverage

• Ligand: rna (8uu4t)

7msct / P9WH41 70SIC in complex with MtbEttA at Pre_R0 state (see paper)
41% identity, 99% coverage

• Ligand: rna (7msct)

C6B32_08820 30S ribosomal protein S20 from Campylobacter fetus subsp. testudinum
36% identity, 98% coverage

• Differentiation of Campylobacter fetus Subspecies by Proteotyping
  Emele, European journal of microbiology & immunology 2019
  • “...CFF8240_0045 ABK83333.1 L24-M 3 CP027287.1:3771937,952 C6B32_00215 AVK80322.1 S20-M 1 CP000487.1:16781911,678,457 CFF8240_1718 ABK82453.1 S20-M 4 CP027287.1:17626181,762,884 C6B32_08820 AVK81906.1 S19-M 1 CP000487.1:3618736,468 CFF8240_0038 ABK81869.1 S19-M 3 CP027287.1:3516035,441 C6B32_00180 AVK80315.1 Table 6. Measured and calculated biomarker masses Biomarker Isoform Measured mass (Da) Standard deviation Measured mass/average mass Monoisotopic mass...”

CFF8240_1718 ribosomal protein S20 from Campylobacter fetus subsp. fetus 82-40
36% identity, 98% coverage

• Differentiation of Campylobacter fetus Subspecies by Proteotyping
  Emele, European journal of microbiology & immunology 2019
  • “...C6B32_00200 AVK80319.1 L24-M 1 CP000487.1:3874638,979 CFF8240_0045 ABK83333.1 L24-M 3 CP027287.1:3771937,952 C6B32_00215 AVK80322.1 S20-M 1 CP000487.1:16781911,678,457 CFF8240_1718 ABK82453.1 S20-M 4 CP027287.1:17626181,762,884 C6B32_08820 AVK81906.1 S19-M 1 CP000487.1:3618736,468 CFF8240_0038 ABK81869.1 S19-M 3 CP027287.1:3516035,441 C6B32_00180 AVK80315.1 Table 6. Measured and calculated biomarker masses Biomarker Isoform Measured mass (Da) Standard deviation...”

CJJ81176_1598 ribosomal protein S20 from Campylobacter jejuni subsp. jejuni 81-176
37% identity, 99% coverage

• High-throughput sequencing of Campylobacter jejuni insertion mutant libraries reveals mapA as a fitness factor for chicken colonization
  Johnson, Journal of bacteriology 2014
  • “...CJJ81176_0444 CJJ81176_0079 CJJ81176_0083 CJJ81176_0357 CJJ81176_1598 CJJ81176_1061 CJJ81176_0813 CJJ81176_1206 CJJ81176_1548 CJJ81176_0508 CJJ81176_1433...”

RR20_SPIOL / P82130 Small ribosomal subunit protein bS20c; 30S ribosomal protein S20, chloroplastic from Spinacia oleracea (Spinach) (see 2 papers)
38% identity, 40% coverage

• function: Component of the chloroplast ribosome (chloro-ribosome), a dedicated translation machinery responsible for the synthesis of chloroplast genome-encoded proteins, including proteins of the transcription and translation machinery and components of the photosynthetic apparatus.
  subunit: Component of the chloroplast small ribosomal subunit (SSU). Mature 70S chloroplast ribosomes of higher plants consist of a small (30S) and a large (50S) subunit. The 30S small subunit contains 1 molecule of ribosomal RNA (16S rRNA) and 24 different proteins. The 50S large subunit contains 3 rRNA molecules (23S, 5S and 4.5S rRNA) and 33 different proteins.

LLNZ_09890 30S ribosomal protein S20 from Lactococcus cremoris subsp. cremoris NZ9000
40% identity, 97% coverage

• Genomics and transcriptomics analysis reveals the mechanism of isobutanol tolerance of a laboratory evolved Lactococcus lactis strain
  Gupta, Scientific reports 2020
  • “...Translation 2 LLNZ_13115 Glyceraldehyde 3-phosphate dehydrogenase Glycolysis/gluconeogenesis 3 LLNZ_08605 50S ribosomal protein L19 Translation 4 LLNZ_09890 30S ribosomal protein S20 Translation 5 LLNZ_08905 30S ribosomal protein S1 Translation 6 LLNZ_03175 Phosphopyruvate hydratase Glycolysis/gluconeogenesis 7 LLNZ_01555 30S ribosomal protein S4 Translation 8 LLNZ_10460 50S ribosomal protein L20...”

5mmjt Structure of the small subunit of the chloroplast ribosome (see paper)
38% identity, 69% coverage

• Ligand: rna (5mmjt)

M6_Spy0935 30S ribosomal protein S20 from Streptococcus pyogenes MGAS10394
40% identity, 97% 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
  • “...1.53 Sortase M6_Spy0872 1.92 Lactoylglutathione lyase M6_Spy0900 1.52 Hypothetical protein M6_Spy0903 1.52 Phage transcriptional repressor M6_Spy0935 1.58 30S ribosomal protein S20 M6_Spy0965 2.41 Integral membrane 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...”

L0397 30S ribosomal protein S20 from Lactococcus lactis subsp. lactis Il1403
42% identity, 97% coverage

• Strain-Dependent Transcriptome Signatures for Robustness in Lactococcus lactis
  Dijkstra, PloS one 2016
  • “...1.5 L113377 ps221 prophage ps2 protein 21 negative 0.4 L77017 ykhJ hypothetical protein negative 0.3 L0397 rpsT 30S ribosomal protein S20 negative 17.7 L0275 dnaN DNA polymerase III subunit beta positive 6.1 L0063 aroF phospho-2-dehydro-3-deoxyheptonate aldolase negative 5.2 L193734 pdc phenolic acid decarboxylase negative 0.3 L156445...”

FE46_RS09040, FP1397 30S ribosomal protein S20 from Flavobacterium psychrophilum
38% identity, 100% coverage

• Dual RNA-Seq of Flavobacterium psychrophilum and Its Outer Membrane Vesicles Distinguishes Genes Associated with Susceptibility to Bacterial Cold-Water Disease in Rainbow Trout (Oncorhynchus mykiss)
  Chapagain, Pathogens (Basel, Switzerland) 2023
  • “...L27, and 50S ribosomal protein L32. For instance, the transcript encoding 30S ribosomal protein S20 (FE46_RS09040) was ranked second among the most enriched in the OMVs (enrichment fold-change ~236). The enrichment of the ribosome components perhaps facilitates the production of more virulence factors necessary to hijack...”
  • “...ID Gene Description Differential Abundance (OMVs/ Fp Whole Cell) FE46_RS03770 HU family DNA-binding protein 250.39 FE46_RS09040 30S ribosomal protein S20 236.37 FE46_RS03985 KTSC domain-containing protein 124.10 FE46_RS03320 Family outer membrane 61.13 FE46_RS09965 Type B 50S ribosomal L31 43.71 FE46_RS09215 50S ribosomal L33 37.49 FE46_RS12230 50S ribosomal...”
• Stress Tolerance-Related Genetic Traits of Fish Pathogen Flavobacterium psychrophilum in a Mature Biofilm
  Levipan, Frontiers in microbiology 2018
  • “...GO:0019843, GO:0006412 4.05 FP1343 30S ribosomal protein S12 rpsL GO:0015935, GO:0000049, GO:0003735, GO:0019843, GO:0006412 3.68 FP1397 30S ribosomal protein S20 rpsT GO:0005840, GO:0003735, GO:0019843, GO:0006412 3.51 FP1432 50S ribosomal protein L33 rpmG GO:0005840, GO:0003735, GO:0006412 3.52 FP1466 Extracytoplasmic function (ECF)-type sigma factor FP1466, FPSM_01934 GO:0003677, GO:0003700,...”

Q9Z7F2 Small ribosomal subunit protein bS20 from Chlamydia pneumoniae
35% identity, 81% coverage

• Prediction of Chlamydia pneumoniae protein localization in host mitochondria and cytoplasm and possible involvements in lung cancer etiology: a computational approach
  Alshamsan, Saudi pharmaceutical journal : SPJ : the official publication of the Saudi Pharmaceutical Society 2017
  • “...RNA-binding proteins. For instant, 30S ribosomal protein S1 (Q9Z8M3), S6 (Q9Z6V5), S5 (Q9Z7S3), and S20 (Q9Z7F2) are needed to express the mRNA with ShineDalgarno sequence. Similarly, various 50S ribosomal proteins are predicted in our study including L10 (Q9Z9A2), L9 (Q9Z6V3), L4 (Q9Z7Q8), L5 (Q9Z7R9), L29 (Q9Z7R5),...”

RR20_ARATH / Q9ASV6 Small ribosomal subunit protein bS20c; 30S ribosomal protein S20, chloroplastic from Arabidopsis thaliana (Mouse-ear cress) (see paper)
AT3G15190 chloroplast 30S ribosomal protein S20, putative from Arabidopsis thaliana
40% identity, 37% coverage

• function: Binds directly to 16S ribosomal RNA.
  subunit: Part of the 30S ribosomal subunit.
  disruption phenotype: Embryonic lethality. Embryo development arrested at the globular stage.
• Genetic factors acting prior to dormancy in sour cherry influence bloom time the following spring
  Goeckeritz, Journal of experimental botany 2024
  • “...July 18 3.75.1 hotpink 30S ribosomal protein S20 Frame shift, potential cis -regulatory elements upstream AT3G15190 Pcer_024813-RA June 12 June 29 July 18 2.25.6 hotpink Terpene synthase family, metal binding domain Two AA changes AT5G23960, AT5G48110 Pcer_097525-RA June 12 June 29 July 18 23.7 hotpink Terpene...”
• Weighted Gene Correlation Network Analysis (WGCNA) of Arabidopsis Somatic Embryogenesis (SE) and Identification of Key Gene Modules to Uncover SE-Associated Hub Genes
  de, International journal of genomics 2022
  • “...( PRXQ /AT3G26060), PHOTOSYNTHETIC NDH SUBCOMPLEX L 4 ( PnsL4/ AT4G39710), PLASTID RIBOSOMAL PROTEIN S20 (AT3G15190), STO (AT1G06040), SINAPOYLGLUCOSE 1 ( SNG1 /AT2G22990), THYLAKOID RHODANESE-LIKE ( TROL /AT4G01050), TONOPLAST INTRINSIC PROTEIN 2 ( TIP2 /AT3G26520), AT3G50685 , AT4G33666 , AT5G16010 , and AT5G54540 genes showed a...”
• Plastid ribosome protein L5 is essential for post-globular embryo development in Arabidopsis thaliana
  Dupouy, Plant reproduction 2022
  • “...ATCG00650 Essential Rogalski et al. ( 2006 ) S19 Essential ATCG00820 NA NA S20 NA AT3G15190 Essential Romani et al. ( 2012 ) S21 NA AT3G27160 Non-essential Morita-Yamamuro et al. ( 2004 ) L1 NA AT3G63490 Essential Bryant et al. ( 2011 ); Romani et al....”
• The ArathEULS3 Lectin Ends up in Stress Granules and Can Follow an Unconventional Route for Secretion
  Dubiel, International journal of molecular sciences 2020
  • “...factor 1-alpha 1/2/3 A1/A2/A3 107.2 At4g23680 At4g23680 F9D16_150 12.4 At5g43940 S-(hydroxymethyl)glutathione dehydrogenase GSNORI ADH2 33.1 At3g15190 30S ribosomal protein S20 RPS20 34.4 At3G04790 Probable ribose-5-phosphate isomerase 3 RPI3 41.0 At1G20620 Catalase-3 CAT3 170.6 At3g01780 Protein TPLATE TPLATE 25.4 At2g20420 Succinate--CoA ligase [ADP-forming] subunit beta At2g20420 323.3...”
• Separation and Paired Proteome Profiling of Plant Chloroplast and Cytoplasmic Ribosomes
  Firmino, Plants (Basel, Switzerland) 2020
  • “...NA ATCG00650 plastid 30S bS18c RPS18 + NA ATCG00820 plastid 30S uS19c RPS19 + NA AT3G15190 plastid 30S bS20c RPS20 + NA AT3G27160 plastid 30S bS21c RPS21 GHS1 + NA AT2G38140 plastid 30S bTHXc PSRP-4 + NA AT3G52150 plastid 30S cS22 PSRP-2 + NA AT1G68590 plastid...”
• Integrated Transcriptional and Proteomic Profiling Reveals Potential Amino Acid Transporters Targeted by Nitrogen Limitation Adaptation
  Liao, International journal of molecular sciences 2020
  • “...S17 2.36 0.002 5.52 0.001 At4g29060 elongation factor Ts family protein 2.52 0.003 4.68 0.004 At3g15190 chloroplast 30S ribosomal protein S20 2.53 0.002 7.40 0.003 At2g24090 ribosomal protein L35 family protein 2.54 0.001 6.40 0.003 At4g24770 RNA-binding protein cp31 2.59 0.001 5.50 0.004 At3g52380 RNA-binding protein...”
• Selection of reference genes for quantitative real-time PCR normalization in Narcissus pseudonarcissu in different cultivars and different organs
  Li, Heliyon 2018
  • “...Ubiquinol-cytochrome C reductase AT3G52730 CATAATCCACAGCCCGTTCT 59.96 165 GATCCAGATTGGGGGAAAAT 59.96 30S RPS20 30S ribosomal protein S20 AT3G15190 TCCAGCAAAGAAGGCAGATT 59.96 157 ATCGGCTTGTGCTTCAGTCT 60.02 eIF-4a Eukaryotic initiation factor 4a AT3G13920 GGTCCTCTCCAAGTCAGGAT 58.1 221 GCAATATAACCTTCCGAGCA 57.87 18S rRNA 18S ribosomal RNA AT3G41768 CCTTGTTGAACAGCGAAAGA 59.05 157 GGGAAGGATGACGATGAGAT 58.89 2.4 Quantitative real-time...”
• Transcriptional analysis of sweet orange trees co-infected with 'Candidatus Liberibacter asiaticus' and mild or severe strains of Citrus tristeza virus
  Fu, BMC genomics 2017
  • “...ribosomal protein S13, chloroplast (CS13) 1.39 RPS17 orange1.1g033970m AT1G79850 ribosomal protein S17 1.48 RPS20 orange1.1g029900m AT3G15190 chloroplast 30S ribosomal protein S20, putative 1.11 1.69 RPS1 orange1.1g015066m AT5G30510 ribosomal protein S1 1.57 GHS1/S21 orange1.1g030080m AT3G27160 glucose hypersensitive1, structural constituent of ribosome 1.86 RPS4B orange1.1g024793m AT5G07090 40S ribosomal...”
• More
• Proteomic Insight into the Response of Arabidopsis Chloroplasts to Darkness
  Wang, PloS one 2016
  • “...30S ribosomal protein S5 (RPS5) P93014 AT2G33800 R 0.350.00 10 30S ribosomal protein S20 (RPS20) Q9ASV6 AT3G15190 R 0.440.02 11 50S ribosomal protein L1(RPL1) Q9LY66 AT3G63490 R 0.500.04 12 50S ribosomal protein L2 (RPL2) P56791 ATCG00830 R 0.700.03 13 Ribosomal protein L4 (RPL4) Q0WW46 AT1G07320 R...”

4v61AT 4v61AT (see paper)
40% identity, 73% coverage

• Ligand: rna (4v61AT)

Q831Q7 Small ribosomal subunit protein bS20 from Enterococcus faecalis (strain ATCC 700802 / V583)
EF2443 ribosomal protein S20 from Enterococcus faecalis V583
IUJ47_RS14095 30S ribosomal protein S20 from Enterococcus faecalis
42% identity, 92% coverage

• Identification and comparison of protein composition of biofilms in response to EGCG from <i>Enterococcus faecalis</i> and <i>Staphylococcus lugdunensis</i>, which showed opposite patterns in biofilm-forming abilities
  Cho, Biofilm 2024
  • “...ribosomal protein L9 14.12 18.80 1.33 Q838B7 EF_0655 Nitroreductase family protein, putative 14.09 18.48 1.31 Q831Q7 rpsT 30S ribosomal protein S20 15.91 20.46 1.29 Q836T3 ppdK Pyruvate, phosphate dikinase 18.35 22.52 1.23 Q834R9 EF_1191 DegV family protein 20.47 24.50 1.20 Q82ZC9 uxuA Mannonate dehydratase 18.67 22.26...”
• The Response of Enterococcus faecalis V583 to Chloramphenicol Treatment
  Aakra, International journal of microbiology 2010
  • “...0.73 0.70 0.89 0.84 1.08 1.15 EF2420 Homoserine kinase 0.63 0.55 0.71 0.69 1.28 1.28 EF2443 Ribosomal protein S20 0.81 0.76 0.80 0.81 1.83 1.84 EF2633 Chaperonin 0.56 0.52 0.89 0.89 2.79 2.67 EF2634 Chaperonin 0.87 0.90 0.99 1.00 2.11 1.83 EF2868 Conserved hypothetical protein 0.57...”
• Antibacterial Components and Modes of the Methanol-Phase Extract from Commelina communis Linn
  Liu, Plants (Basel, Switzerland) 2023
  • “...ribosomal protein S11 IUJ47_RS04545 0.248 30S ribosomal protein S19 IUJ47_RS04550 0.252 50S ribosomal protein L22 IUJ47_RS14095 0.252 30S ribosomal protein S20 IUJ47_RS04585 0.259 50S ribosomal protein L5 IUJ47_RS04535 0.26 50S ribosomal protein L23 IUJ47_RS04590 0.261 Type Z 30S ribosomal protein S14 IUJ47_RS04525 0.264 50S ribosomal protein...”

B2I23_RS02910 30S ribosomal protein S20 from Candidatus Liberibacter asiaticus
38% identity, 88% coverage

• The Genome of "Candidatus Liberibacter asiaticus" Is Highly Transcribed When Infecting the Gut of Diaphorina citri
  Darolt, Frontiers in microbiology 2021
  • “...transfer-messenger RNA ssrA (B2I23_RS04260), rnpB RNAse P (B2I23_RS04605), and ribosomal proteins rpmJ (B2I23_RS00165) and rpsT (B2I23_RS02910) genes. The chaperone gene for the cold shock domain-containing protein (B2I23_RS04040) is among the most expressed in Las III. The classification of genes mapped in the COGs ( Tatusov et...”

Q8DZZ2 Small ribosomal subunit protein bS20 from Streptococcus agalactiae serotype V (strain ATCC BAA-611 / 2603 V/R)
38% identity, 92% coverage

• Downregulation of Ribosomal Contents and Kinase Activities Is Associated with the Inhibitive Effect on the Growth of Group B Streptococcus Induced by Placental Extracellular Vesicles
  Gao, Biology 2021
  • “...structural constituent of ribosome Q8DYG1 down 50S ribosomal protein L11, large ribosomal subunit rRNA binding Q8DZZ2 down 30S ribosomal protein S20, rRNA binding R4Z934 down 30S ribosomal protein S11, rRNA binding V6YZ47 down 50S ribosomal protein L3, rRNA binding V6YZ80 down 30S ribosomal protein S13, RNA/tRNA...”

SACOL1642 ribosomal protein S20 from Staphylococcus aureus subsp. aureus COL
Q99TR3 Small ribosomal subunit protein bS20 from Staphylococcus aureus (strain Mu50 / ATCC 700699)
SA1414 30S ribosomal protein S20 from Staphylococcus aureus subsp. aureus N315
SAUSA300_1545 30S ribosomal protein S20 from Staphylococcus aureus subsp. aureus USA300_FPR3757
EKM74_RS01310 30S ribosomal protein S20 from Staphylococcus aureus
40% identity, 95% coverage

• The Staphylococcus aureus LytSR two-component regulatory system affects biofilm formation
  Sharma-Kuinkel, Journal of bacteriology 2009
  • “...SACOL2214 SACOL0591 SACOL2226 SACOL1292 SACOL2230 SACOL2235 SACOL1642 SA0352 SACOL2225 SACOL0590 SACOL0593 SACOL1727 SACOL0958 rplE rplF rplJ rplM rplN...”
• Structural and Functional Dynamics of Staphylococcus aureus Biofilms and Biofilm Matrix Proteins on Different Clinical Materials
  Hiltunen, Microorganisms 2019
  • “...Q6GJV1 30S ribosomal protein S19 Q6GEI7 30S ribosomal protein S2 Q6GHH9 30S ribosomal protein S20 Q99TR3 30S ribosomal protein S21 Q6GGC5 30S ribosomal protein S3 Q6GEI9 30S ribosomal protein S4 Q6GFY8 30S ribosomal protein S5 Q6GEK0 30S ribosomal protein S6 Q6GJV3 30S ribosomal protein S7 Q6GJC2...”
• Analysis of the matrix-assisted laser desorption ionization-time of flight mass spectrum of Staphylococcus aureus identifies mutations that allow differentiation of the main clonal lineages
  Josten, Journal of clinical microbiology 2013
  • “...antisense products rpmJ (SAS078) SAR1012 rpmC (SA2039) rpsT (SA1414) hup (SA1305) Primers used for PCR and sequencing of genes hld (SAOUHSC_02260) graF (SAS030)...”
  • “...(SAS044) graC (SAS044) SA0772 rpmC (SA2039) rpmC (SA2039) rpmC (SA2039) rpsT (SA1414) s s s k k s s k 5.16 9.52 9,627 hup (SA1305) k 9.52 10,105 rpsP (SA1081)...”
• Transcriptional profiles of the response of methicillin-resistant Staphylococcus aureus to pentacyclic triterpenoids
  Chung, PloS one 2013
  • “...rpsS 30S ribosomal protein S19 4.8 Translation SA1099 rpsB 30S ribosomal protein S2 9.9 Translation SA1414 rpsT 30S ribosomal protein S20 6.6 Translation SA1404 rpsU 30S ribosomal protein S21 12.9 Translation SAS052 rpsD 30S ribosomal protein S4 5.7 Translation SA0496 rplA 50S ribosomal protein L1 6.1...”
• Characterizing the effects of inorganic acid and alkaline shock on the Staphylococcus aureus transcriptome and messenger RNA turnover
  Anderson, FEMS immunology and medical microbiology 2010
  • “...putative membrane-associated zinc metalloprotease sa_c1852s1575_a_at 2.7 2.5 2.5 SA1412 hydrolase-related protein sa_c1866s1587_a_at 5.6 2.5 ND SA1414 peptide ABC transporter sa_c1870s1592_a_at 4.9 2.5 ND SA1415 peptide ABC transporter sa_c1872s1598_a_at 7.6 2.5 ND SA1416 putative peptide ABC transporter sa_c1876s1602_a_at 6.9 2.5 ND SA1417 peptide ABC transporter sa_c2551s9779_a_at 2.1...”
• Characterizing the effect of the Staphylococcus aureus virulence factor regulator, SarA, on log-phase mRNA half-lives
  Roberts, Journal of bacteriology 2006
  • “...SA0504 SA2034 SA2024 SA0503 SA2025 SAS079 SA2038 SA1414 SA0506 SA0506 SA0506 SA0502 Translation elongation factor EF-P Translational elongation factor G...”
• Dual Gene Expression Analysis Identifies Factors Associated with Staphylococcus aureus Virulence in Diabetic Mice
  Jacquet, Infection and immunity 2019
  • “...SAUSA300_0080 SAUSA300_0068 SAUSA300_1511 SAUSA300_1541 SAUSA300_1545 SAUSA300_0781 SAUSA300_1542 SAUSA300_2195 SAUSA300_1540 SAUSA300_0884 Downregulated...”
• Transcriptomic Analysis Revealed Antimicrobial Mechanisms of Lactobacillus rhamnosus SCB0119 against Escherichia coli and Staphylococcus aureus
  Peng, International journal of molecular sciences 2022
  • “...biotin carboxylase subunit EKM74_RS01125 36.7 12.69 642.43 184.29 4.129847 rpmG ; 50S ribosomal protein L33 EKM74_RS01310 21.83 0.96 168.95 53.18 2.951911 rpsT ; 30S ribosomal protein S20 EKM74_RS01660 458.35 97.45 2756.92 263.1 2.588527 rpmA ; 50S ribosomal protein L27 EKM74_RS01670 102.05 29.64 4057 488.97 5.313122 rplU...”

G7LDS2 30S ribosomal protein S20 from Medicago truncatula
34% identity, 43% coverage

• Proteomic analysis of the response of Funnelifor mismosseae/Medicago sativa to atrazine stress
  Sui, BMC plant biology 2018
  • “...5 Medicago truncatula MTR_2g435490 20.192 8.221 1.726 0.010 Proteins involved in translation, synthesis and processing G7LDS2 30S ribosomal protein S20 Medicago truncatula MTR_8g061350 19.108 10.580 1.346 0.024 A0A072VKA9 50S ribosomal protein L11P Medicago truncatula MTR_1g060610 16.183 9.994 0.629 0.006 A0A072URU1 60S ribosomal protein L242 Medicago truncatula...”

BL0849 30S ribosomal protein S20 from Bifidobacterium longum NCC2705
50% identity, 100% coverage

• Genomics of Actinobacteria: tracing the evolutionary history of an ancient phylum
  Ventura, Microbiology and molecular biology reviews : MMBR 2007
  • “...the universally conserved alpha-sarcin loop BL0849 ......................................RpsT; COG family, ribosomal protein S20; PFAM_ID, Ribosomal_S20p BL0859...”

6w6pt / A0A1B4XQJ7 6w6pt (see paper)
42% identity, 90% coverage

• Ligand: rna (6w6pt)

SUB0956 30S ribosomal protein S20 from Streptococcus uberis 0140J
39% identity, 97% coverage

• Prediction of Streptococcus uberis clinical mastitis treatment success in dairy herds by means of mass spectrometry and machine-learning
  Maciel-Guerra, Scientific reports 2021
  • “...to three proteins (SUB0086, SUB1598 and SUB0788), peak 8139.57Da could be matched to three proteins (SUB0956, SUB0512 and SUB0090) and peak 9487.76Da could be matched to two proteins (SUB1267 and SUB0408). While peaks 5377.47Da, 6717.79Da, 6841.15Da and 7905.41Da matched to one protein in S. uberis 0140J...”
  • “...proteins (SUB1659A, SUB0086, SUB1795 and SUB0076) two of them were 30S ribosomal proteins (SUB0689 and SUB0956), and the four remaining proteins were bacteriocin (SUB0512), translation initiation factor (SUB0090), DNA-binding (SUB1267), and a membrane protein with insertion efficiency factor (SUB0408). The predicted three-dimensional models of these proteins...”

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.