PaperBLAST

PaperBLAST Hits for ABZR87_RS02730 (38 a.a., MKVLASVKRI...)

Show query sequence

>ABZR87_RS02730
MKVLASVKRICRNCKIIKRKGVVRVICSTDPRHKQRQG

Running BLASTp...

Found 50 similar proteins in the literature:

Bxe_A0336 50S ribosomal protein L36 from Burkholderia xenovorans LB400
Bxe_A0336 50S ribosomal protein L36 from Paraburkholderia xenovorans LB400
95% identity, 100% coverage

• The long-chain flavodoxin FldX1 improves the biodegradation of 4-hydroxyphenylacetate and 3-hydroxyphenylacetate and counteracts the oxidative stress associated to aromatic catabolism in Paraburkholderia xenovorans
  Rodríguez-Castro, Biological research 2024
  • “...growth of strain p2- fldX1 on 3-HPA, but not on 4-HPA.The 50S ribosomal protein L36 (Bxe_A0336) were downregulated in the control strain cultured in 3-HPA. More than 20 membrane proteins, including porins and transporters, showed changes in expression during growth of the strains p2- fldX1 and...”

bglu_1g02800 50S ribosomal protein L36 from Burkholderia glumae BGR1
95% identity, 83% coverage

• RNAseq-based Transcriptome Analysis of Burkholderia glumae Quorum Sensing
  Kim, The plant pathology journal 2013
  • “...0.8 1.2 1.2 bglu_1g02760 rpm 1.3 0.7 1. 1 bglu_1g02770 rplO 1.2 0.6 1.3 1.3 bglu_1g02800 rpmJ 1.3 1 1.3 1.4 bglu_1g02810 rpsM 1.1 0.7 1.4 1.4 bglu_1g02820 rpsK 1.1 0.8 1.3 1.2 bglu_1g02830 rpsD 1.1 0.7 1 1.2 bglu_1g02850 rplQ 0.8 0.4 1.3 1.3 bglu_1g04830...”

PP0475 ribosomal protein L36 from Pseudomonas putida KT2440
PP_0475 50S ribosomal protein L36 from Pseudomonas putida KT2440
82% identity, 100% coverage

• UEG Week 2024 Poster Presentations
  , United European gastroenterology journal 2024
• UEG Week 2023 Poster Presentations
  , United European gastroenterology journal 2023
• PpoR is a conserved unpaired LuxR solo of Pseudomonas putida which binds N-acyl homoserine lactones
  Subramoni, BMC microbiology 2009
  • “...PP5168 sulfate ABC transporter, ATP-binding protein 2.297 22. PP0466 50S ribosomal protein L5 2.236 23. PP0475 50S ribosomal protein L36 2.213 24. PP1600 outer membrane protein OmpH 2.205 25. PP1464 tRNA (guanine-N(1)-)-methyltransferase 2.181 26. PP0454 50S ribosomal protein L3 2.178 27. PP0689 50S ribosomal protein L27...”
• 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 L6 PP_0472 rpmD 50S ribosomal protein L30 PP_0473 rplO 50S ribosomal protein L15 PP_0475 rpmJ 50S ribosomal protein L36 PP_0476 rpsM 30S 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...”

YPO0230 50S ribosomal protein L36 from Yersinia pestis CO92
YPTB3677 50S ribosomal protein L36 from Yersinia pseudotuberculosis IP 32953
79% identity, 100% coverage

• Characterization of Zur-dependent genes and direct Zur targets in Yersinia pestis
  Li, BMC microbiology 2009
  • “...(YPO0111) and YkgM (YPO3134) in Y. pestis , while those of L36 protein are RpmJ (YPO0230) and RpmJ2 (YPO3135) [ 17 ]. YkgM and RpmJ2 are the C- forms of corresponding ribosomal proteins. ykgM and rpmJ2 constitutes a putative ykgM - rpmJ2 operon in Y. pestis...”
• Tissue dual RNA-seq allows fast discovery of infection-specific functions and riboregulators shaping host-pathogen transcriptomes
  Nuss, Proceedings of the National Academy of Sciences of the United States of America 2017
  • “...to their paralogs encoded by YPTB0102 (RpmE) and YPTB3677 (RpmJ). Recent studies in E. coli and Bacillus subtilis suggested that the zinccontaining RpmE protein...”

8cd16 / Q9HWF6 8cd16 (see paper)
PA4242 50S ribosomal protein L36 from Pseudomonas aeruginosa PAO1
Q9HWF6 Large ribosomal subunit protein bL36A from Pseudomonas aeruginosa (strain ATCC 15692 / DSM 22644 / CIP 104116 / JCM 14847 / LMG 12228 / 1C / PRS 101 / PAO1)
79% identity, 100% coverage

• Ligand: rna (8cd16)
• Calprotectin-Mediated Zinc Chelation Inhibits Pseudomonas aeruginosa Protease Activity in Cystic Fibrosis Sputum
  Vermilyea, Journal of bacteriology 2021 (secret)
• Strategies for Zinc Uptake in Pseudomonas aeruginosa at the Host-Pathogen Interface
  Wang, Frontiers in microbiology 2021
  • “...RpmE2 and RpmJ2 are homologous proteins of the 50S ribosomal proteins RpmE (PA5049) and RpmJ (PA4242) in P. aeruginosa ( Pederick et al., 2015 ). There are usually two forms of prokaryotic ribosomal proteins, the C + subtype that binds metal ions such as Zn 2+...”
• Global Analysis of the Zinc Homeostasis Network in Pseudomonas aeruginosa and Its Gene Expression Dynamics
  Ducret, Frontiers in microbiology 2021
  • “...dksA2 PA5536 Supressor protein rpmE PA5049 Ribosomal protein L31 rpmE2 PA3601 Ribosomal protein L31 rpmJ PA4242 Ribosomal protein L36 rpmJ2 PA3600 Ribosomal protein L36 Others PA2807 PA2807 Copper binding protein oprD PA0958 Outer membrane porin Zn Export Systems Dynamics of CadA and CzcCBA Expression We recently...”
• The Pseudomonas aeruginosa CreBC two-component system plays a major role in the response to β-lactams, fitness, biofilm growth, and global regulation
  Zamorano, Antimicrobial agents and chemotherapy 2014
  • “...PA3873 PA3874 PA3875 PA3876 PA3877 PA3915 PA4110 PA4238 PA4242 PA4246 PA4247 PA4254 PA4257 PA4258 PA4260 PA4262 PA4266 PA4268 PA4272 PA4944 PA5212 creD Inner...”
• 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
  • “...PA3920 PA4031 PA4053 PA4220 PA4238 PA4239 PA4240 PA4241 PA4242 PA4243 PA4245 PA4246 PA4247 PA4248 PA4249 PA4252 PA4254 PA4257 PA4258 PA4259 PA4260 PA4261 PA4262...”
• Top-Down LESA Mass Spectrometry Protein Analysis of Gram-Positive and Gram-Negative Bacteria
  Kocurek, Journal of the American Society for Mass Spectrometry 2017
  • “...room temperature 723.8214 +10 7228.14 -2.0 L35 Q9I0A1 41 -Met 739.5860 +6 4431.47 -1.2 L36 Q9HWF6 45 759.9734 +11 8348.63 -1.4 S21 Q9I5V8 29 -Met 826.5565 +11 9081.04 -0.3 HU- P05384 51 Incubation: 48 h, 37 C Sampled fresh 951.8583 +8 7606.81 0.0 UPF0337 protein PA4738...”

SecX / b3299 50S ribosomal subunit protein L36 from Escherichia coli K-12 substr. MG1655 (see 11 papers)
rpmJ / P0A7Q6 50S ribosomal subunit protein L36 from Escherichia coli (strain K12) (see 13 papers)
RL36_ECOLI / P0A7Q6 Large ribosomal subunit protein bL36A; 50S ribosomal protein L36; Ribosomal protein B from Escherichia coli (strain K12) (see 10 papers)
8a3l3 / P0A7Q6 8a3l3 (see paper)
SENTW_3546 50S ribosomal protein L36 from Salmonella enterica subsp. enterica serovar Weltevreden str.
NP_417758 50S ribosomal subunit protein L36 from Escherichia coli str. K-12 substr. MG1655
STM3419 50S ribosomal subunit protein X from Salmonella enterica subsp. enterica serovar Typhimurium str. LT2
NP_462323 50S ribosomal subunit protein X from Salmonella typhimurium LT2
b3299 50S ribosomal protein L36 from Escherichia coli str. K-12 substr. MG1655
SEN3247 50S ribosomal subunit protein L36 from Salmonella enterica subsp. enterica serovar Enteritidis str. P125109
ECs4164 50S ribosomal subunit protein L36 from Escherichia coli O157:H7 str. Sakai
76% identity, 100% coverage

• function: One of the last ribosomal proteins to be assembled in the 50S subunit, it contacts a number of helices in the 23S rRNA, acting as molecular glue (PubMed:33639093). The simultaneous presence of uL16 and bL36 probably triggers ObgE's GTPase activity and eventual dissociation from the mature 50S ribosomal subunit (PubMed:33639093).
  subunit: Part of the 50S ribosomal subunit.
• Ligands: rna; zinc ion (8a3l3)
• Transcriptional profile of Salmonella enterica subsp. enterica serovar Weltevreden during alfalfa sprout colonization
  Brankatschk, Microbial biotechnology 2014
  • “...rpmF SENTW_2062 6.82 50S ribosomal protein L32 rpmG SENTW_3828 8.15 50S ribosomal protein L33 rpmJ SENTW_3546 5.27 50S ribosomal subunit protein L36 rpsH SENTW_3553 10.11 30S ribosomal protein S8 rpsI SENTW_3473 6.06 30S ribosomal protein S9 rpsK SENTW_3544 5.67 30S ribosomal protein S11 rpsR SENTW_4496 12.63...”
• Nonspecific inhibition of Escherichia coli ornithine decarboxylase by various ribosomal proteins: detection of a new ribosomal protein possessing strong antizyme activity.
  Kashiwagi, Biochimica et biophysica acta 1987 (PubMed)
  • GeneRIF: N-terminus verified by Edman degradation on complete protein
• Conserved intergenic sequences revealed by CTAG-profiling in Salmonella: thermodynamic modeling for function prediction
  Tang, Scientific reports 2017
  • “...intergenic region between tdcA and rnpB 3494593 STM3330 glutamate synthase, large subunit 3585835 STM3418 & STM3419 intergenic region between rpsM and rpmJ 3589847 STM3427 30S ribosomal subunit protein S14 3593146 STM3434 & STM3435 intergenic region between rpsC and rplV 4141162 STM3933 tRNA-Leu 4631227 STM4392 primosomal replication...”
• Salmonella enterica serovar typhimurium colonizing the lumen of the chicken intestine grows slowly and upregulates a unique set of virulence and metabolism genes
  Harvey, Infection and immunity 2011
  • “...Gene STM3430 STM3422 STM4393 STM3441 STM0981 STM3447 STM3448 STM3436 STM3419 STM1335 rplN rplP rpsR rpsJ rpsA rpsG rpsL rpsS rpmJ rpmI 50S 50S 30S 30S 30S 30S...”
• Functional Prediction of Biological Profile During Eutrophication in Marine Environment
  Sbaoui, Bioinformatics and biology insights 2022
  • “...RfbD P37760 TDP-rhamnose synthetase, NAD(P)-binding Rpe P0AG07 Ribulose-5-phosphate 3-epimerase RpiA P0A7Z0 Ribose 5-phosphate isomerase RpmJ P0A7Q6 50S ribosomal subunit protein L36 RpoN P24255 RNA polymerase, sigma 54 (sigma N) factor RseP P0AEH1 Intramembrane zinc metalloprotease RtxA A0A3L0W7I6 Multifunctional-autoprocessing repeats-in-toxin ScpA P27253 Methylmalonyl-coa epimerase SdhA P0AC41 Succinate...”
• Gene socialization: gene order, GC content and gene silencing in Salmonella
  Papanikolaou, BMC genomics 2009
  • “...use one set of codon freqs for all pairs (0/1)? We have removed two genes (NP_462323 and NP_463455) for which the program couldn't provide us with a reliable Ka/Ks ratio, as well as all genes with Ka/Ks = 0 (Additional file 7 ). In order to...”
• Genome-Scale Mapping of Escherichia coli σ54 Reveals Widespread, Conserved Intragenic Binding
  Bonocora, PLoS genetics 2015
  • “...- b3011 yqhD 438 9.586 IA26 3440661 1 T TGGC GCTGTTTA TGC T 3440654 + b3299 rpmJ - b3324 gspC 12927 10.636 IA27 3851258 2 TC GGC ACGAATT TTG AC 3851261 + b4616 istR - b4618 tisB 296 8.863 a Unique ID; IS = Inside a...”
• Analysis of phage Mu DNA transposition by whole-genome Escherichia coli tiling arrays reveals a complex relationship to distribution of target selection protein B, transcription and chromosome architectural elements
  Ge, Journal of biosciences 2011
  • “...2180627 1.47 yegV b2100 12 1989873 1990138 1.45 leuZ b1908 13 3440478 3441055 1.45 rpmJ b3299 14 3886442 3886611 1.45 tnaL b3707 15 1204622 1204815 1.34 ymfR b1150 16 2151536 2151777 1.3 sibB b2074 17 3305802 3306283 1.3 deaD b3162 18 1798352 1798881 1.28 infC b1718...”
• Analysis of promoter targets for Escherichia coli transcription elongation factor GreA in vivo and in vitro
  Stepanova, Journal of bacteriology 2007
  • “...prlA rplO rpmD rpsE rplR rplF rpsH rpsN rplE rplX rplN b3299 b3300 b3301 b3302 b3303 b3304 b3305 b3306 b3307 b3308 b3309 b3310 2.7 4.3 3.1 3.7 3.7 3.1 4.1 3.2...”
• Global gene expression profiling of the asymptomatic bacteriuria Escherichia coli strain 83972 in the human urinary tract
  Roos, Infection and immunity 2006
  • “...c2758 b3310 b3298 b3231 b2621 Z2747 b3320 b3123 b3341 b3299 b2779 b3782 b3983 b2579 b1677 b2153 b0114 b3986 b0169 c4310 b4457 b3301 b2415 b3305 b3637 b1779...”
• Interfering with different steps of protein synthesis explored by transcriptional profiling of Escherichia coli K-12
  Sabina, Journal of bacteriology 2003
  • “...b1444 b1601 b0696 b4017 b0188 b2578 b1749 b3242 b3104 b1736 b3299 b0011 b1447 b3302 b1451 b2261 b0285 b1600 b0174 b2534 b0154 b3312 b1400 82 77 59 28 27 24...”
  • “...b4200 b3313 b3057 b0580 b3312 b0833 b3683 b4159 b4201 b3667 b2451 b3065 b3299 b2033 b3301 b1593 b1416 b1189 46 29 27 27 26 23 23 20 19 18 18 17 17 17 16 16 15...”
• Microarray analysis of orthologous genes: conservation of the translational machinery across species at the sequence and expression level
  Jiménez, Genome biology 2003
  • “...Sll Ribosomal protein 10 b3298 Yes** COG0099 J3 30S ribosomal protein S13 Ribosomal protein 11 b3299 Yes COG0257 J4 50S ribosomal protein X Ribosomal protein 11 b3300 No - - (secY) membrane protein, protein secretion Ribosomal protein 11 b3301 Yes** COG0200 J4 50S ribosomal protein L15...”
• 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
  • “...zwf b3318 b3309 b2185 b3185 b3637 b3302 b3636 b3703 b3299 b3295 b3314 b3296 b3303 b4200 b3341 b3306 b3230 b3321 b3297 b3298 b3307 b2609 b3311 b4202 b3316 b0023...”
• Genome-wide transcriptional profiling of the Escherichia coli responses to superoxide stress and sodium salicylate
  Pomposiello, Journal of bacteriology 2001
  • “...b3186 b3315 b3318 b3309 b3185 b3637 b3312 b3302 b1717 b3299 b3295 b0169 b3314 b3296 b3303 b3306 b3230 b3321 b3297 b3307 b2609 b3311 atpA atpC atpF atpH atpI...”
• Global transcriptomic analysis of ethanol tolerance response in Salmonella Enteritidis
  He, Current research in food science 2022
  • “...rpoC 2.62 DNA-directed RNA polymerase subunit beta' Translation SEN3254 rpsH 4.10 30S ribosomal protein S8 SEN3247 rpmJ 4.49 50S ribosomal protein L36 SEN3178 rplM 3.19 50S ribosomal protein L13 SEN3258 rplN 2.48 50S ribosomal protein L14 SEN2597 rpsP 3.06 30S ribosomal protein S16 SEN3934 rplA 3.52...”
• Global transcriptional response of Escherichia coli O157:H7 to growth transitions in glucose minimal medium
  Bergholz, BMC microbiology 2007
  • “...rpsD -2.17 1 ECs5046 yjcD -3.81 1 ECs4162 rpsK -2.36 1 ECs5051 acs 5.55 2 ECs4164 rpmJ -2.03 1 ECs5067 O157 2.21 2 ECs4165 prlA -2.53 1 ECs5153 purA -2.06 1 ECs5164 yjfN 4.54 2 ECs5240 yjgR 2.24 2 ECs5192 cysQ 2.01 2 ECs5259 O157 -2.09...”

HI0798.1 ribosomal protein L36 (rpL36) from Haemophilus influenzae Rd KW20
79% identity, 100% coverage

• Initial proteome analysis of model microorganism Haemophilus influenzae strain Rd KW20
  Kolker, Journal of bacteriology 2003
  • “...HI0789 HI1630 HI0879 HI0951 HI0785 HI0796 HI0758 HI0158 HI0950 HI0998 HI1319m HI0798.1 550 252 236 207 167 131 157 131 131 119 130 125 123 102 90 83 86 76 92 90...”

7m4v3 / B7IA18 A. Baumannii ribosome-eravacycline complex: 50s (see paper)
ACIAD3198 50S ribosomal protein L36 from Acinetobacter sp. ADP1
AbA118F_2920 50S ribosomal protein L36 from Acinetobacter baumannii
74% identity, 100% coverage

• Ligands: rna; zinc ion (7m4v3)
• iTRAQ-Based Comparative Proteomic Analysis of Acinetobacter baylyi ADP1 Under DNA Damage in Relation to Different Carbon Sources
  Jiang, Frontiers in microbiology 2019
  • “...30S ribosomal protein S13 rpsM ACIAD3197 0.55 0.48 0.5 0.64 50S ribosomal protein L36 rpmJ ACIAD3198 0.48 0.82 0.61 0.68 50S ribosomal protein L15 rplO ACIAD3200 0.6 0.59 0.47 0.53 50S ribosomal protein L30 rpmD ACIAD3201 0.77 0.73 0.62 0.73 30S ribosomal protein S5 rpsE ACIAD3202...”
• Cerebrospinal fluid (CSF) augments metabolism and virulence expression factors in Acinetobacter baumannii
  Martinez, Scientific reports 2021
  • “...AbA118F_0149 1.58 8.3 E-26 Imidazolonepropionase AbA118F_2323 pgaC 1.56 2.8 E-13 Biofilm PGA synthesis N-glycosyltransferase PgaC AbA118F_2920 1.56 6.5 E-44 LSU ribosomal protein L36p : LSU ribosomal protein L36p, zinc-dependent AbA118F_1621 1.55 4.6 E-54 Glyceraldehyde-3-phosphate dehydrogenase, putative AbA118F_1623 1.55 2.0 E-43 Gluconate transporter family protein AbA118F_3243 1.54...”

VC2575 ribosomal protein L36 from Vibrio cholerae O1 biovar eltor str. N16961
B7C60_RS03515 50S ribosomal protein L36 from Vibrio fujianensis
82% identity, 100% coverage

• A systems biology approach to modeling vibrio cholerae gene expression under virulence-inducing conditions
  Kanjilal, Journal of bacteriology 2010
  • “...VCA0817 VCA0932 VC0013 VC0324 VC0326 VC0361 VC0570 VC2342 VC2575 VC2585 VC2590 VC2596 VC0797 VC1843 VC2295 VC2542 VC2698 VC2699 VC2768 VC2770 VCA1060 VC0481...”
• Comparative Genomics and Transcriptomics Analyses Reveal a Unique Environmental Adaptability of Vibrio fujianensis
  Huang, Microorganisms 2020
  • “...rpsG small subunit ribosomal protein S7 Translation B7C60_RS03490 rplQ large subunit ribosomal protein L17 Translation B7C60_RS03515 rpmJ large subunit ribosomal protein L36 Translation B7C60_RS03525 rplO large subunit ribosomal protein L15 Translation B7C60_RS03530 rpmD large subunit ribosomal protein L30 Translation B7C60_RS03535 rpsE small subunit ribosomal protein S5...”

Alvin_2342 ribosomal protein L36 from Allochromatium vinosum DSM 180
79% identity, 100% coverage

• Genome-wide transcriptional profiling of the purple sulfur bacterium Allochromatium vinosum DSM 180T during growth on different reduced sulfur compounds
  Weissgerber, Journal of bacteriology 2013
  • “...Alvin_2337 Alvin_2338 Alvin_2339 Alvin_2340 Alvin_2341 Alvin_2342 Alvin_2343 Alvin_2357 Alvin_2358 Alvin_2359 Alvin_2360 Alvin_2361 Alvin_2362 Alvin_2363...”

FTT_0346 50S ribosomal protein L36 from Francisella tularensis subsp. tularensis SCHU S4
82% identity, 100% coverage

• Global Analysis of Genes Essential for Francisella tularensis Schu S4 Growth In Vitro and for Fitness during Competitive Infection of Fischer 344 Rats
  Ireland, Journal of bacteriology 2019
  • “...value cutoff to 1E05 and without using the low-complexity filter. Nine genes returned hits, including FTT_0346 ( rpmJ ), FTT_0801c, FTT_0839 ( tolA ), FTT_1030, FTT_1275 ( mglA ), FTT_1453c ( wzx ), FTT_1457c ( wbtG ), FTT_1607 ( minE ), and FTT_1730c, and were therefore...”

SO0252 ribosomal protein L36 from Shewanella oneidensis MR-1
79% identity, 100% coverage

• Transcriptome analysis reveals a stress response of Shewanella oneidensis deprived of background levels of ionizing radiation
  Castillo, PloS one 2018
  • “...protein S5 -1.04 SO0249 rpmD Ribosomal protein L30 -1.13 SO0250 rplO Ribosomal protein L15 -1.15 SO0252 rpmJ Ribosomal protein L36 -1.01 -1.07 SO0253 rpsM Ribosomal protein S13 -1.02 SO0257 rplQ Ribosomal protein L17p -1.04 -1.51 SO0513 yaeJ Peptidyl-tRNA hydrolyzing factor 1.09 SO0604 hflX GTP-binding protein -1.04...”

LOC18054512 uncharacterized protein LOC18054512 from Citrus x clementina
63% identity, 29% coverage

• Transcriptome analysis of Harumi tangor fruits: Insights into interstock-mediated fruit quality
  Liao, Frontiers in plant science 2022
  • “...the HP1 group, including ciclev10033291m, 50 S ribosomal protein L5 (LOC18046626), RPL18 (LOC18048753), and RPL36 (LOC18054512). However, the expression of genes encoding other ribosomal proteins were inhibited in the HPP2 group, including RPS30C (LOC18055660), RPL34A (LOC18048110), ARS27A (ciclev10017430m), RS21 (LOC18041783), and a hypothetical protein (ciclev10003310m). Several...”

SP60_05345 50S ribosomal protein L36 from Candidatus Thioglobus autotrophicus
82% identity, 100% coverage

• Metabolic flexibility of SUP05 under low DO growth conditions
  Mattes, Environmental microbiology 2021
  • “...0.028 0.001 0.001 SP60_05335 ALE52677.1 50S ribosomal protein L15 0.006 0.002 0.050 0.044 0.001 0.001 SP60_05345 ALE52679.1 50S ribosomal protein L36 0.005 0.001 0.029 0.102 0.011 0.007 SP60_05680 ALE53249.1 NADH:ubiquinone oxidoreductase 0.005 0.001 0.021 0.044 0.012 0.008 SP60_05980 NA tRNA-Gly 0.003 0.004 0.022 0.617 0.006 0.002...”

8rd8ep / A0A0M4U3Z5 8rd8ep (see paper)
66% identity, 100% coverage

• Ligand: rna (8rd8ep)

HP1297 ribosomal protein L36 (rpl36) from Helicobacter pylori 26695
P56058 Large ribosomal subunit protein bL36 from Helicobacter pylori (strain ATCC 700392 / 26695)
74% identity, 100% coverage

• Insight into the essential role of the Helicobacter pylori HP1043 orphan response regulator: genome-wide identification and characterization of the DNA-binding sites
  Pelliciari, Scientific reports 2017
  • “...amplified by PCR with oligonucleotides 1296FPF/1296FPR. This region encompasses the putative promoter region of HPG27_RS06525 (HP1297 according to 26695 annotation). This work pGEMp1260 pGEM-T-Easy derivative, containing a 242bp DNA fragment corresponding to the region from 1.321.773 to 1.322.015 of H. pylori G27 genome amplified by PCR...”
• New implications on genomic adaptation derived from the Helicobacter pylori genome comparison
  Lara-Ramírez, PloS one 2011
  • “...have not been annotated in some strains, including two ribosomal proteins, L34 (HP1447) and L36 (HP1297); most of false core genes came from the published data, including pseudogens particularly due to frameshifts in some strains and size-different genes. As for the gene HP0326, it is a...”
• Toward Spectral Library-Free Matrix-Assisted Laser Desorption/Ionization Time-of-Flight Mass Spectrometry Bacterial Identification
  Cheng, Journal of proteome research 2018
  • “...information contained in protein sequences database, that is, SwissProt. They chose 35 biomarkers, for example, P56058, P56056, O25662, O25451, etc., to identify Helicobacter pylori . In 2003, the same research team 20 extended this approach to four genera, that is, Bacillus , Escherichia , Pseudomonas ,...”

AT5G20180 ribosomal protein L36 family protein from Arabidopsis thaliana
63% identity, 37% coverage

• Plastid ribosome protein L5 is essential for post-globular embryo development in Arabidopsis thaliana
  Dupouy, Plant reproduction 2022
  • “...NA NA L35 NA AT2G24090 Essential Romani et al. ( 2012 ) L36 NA ATCG00760/ AT5G20180 Non-essential Fleischmann et al. ( 2011 ) Overview of experimentally demonstrated essentiality of Plastid Ribosomal Proteins (PRPs) for embryogenesis and cell survival in A. thaliana. The essentiality of plastid ribosomal...”
• Spaceflight induces novel regulatory responses in Arabidopsis seedling as revealed by combined proteomic and transcriptomic analyses
  Kruse, BMC plant biology 2020
  • “...50S ribosomal protein L24, chloroplastic 1.01 0.012 AT1G79850 30S ribosomal protein S17, chloroplastic 1.02 0.002 AT5G20180 Ribosomal protein L36 1.03 0.019 AT5G40950 50S ribosomal protein L27, chloroplastic 1.05 0.002 AT2G24090 Ribosomal protein L35 1.06 0.001 AT4G11175 Translation initiation factor IF-1, chloroplastic 1.08 0.002 AT3G27160 Ribosomal protein...”
• An Update on Mitochondrial Ribosome Biology: The Plant Mitoribosome in the Spotlight
  Tomal, Cells 2019
  • “...bL27m AT2G16930 bL28m AT4G31460 uL29m AT1G07830 uL30m AT5G55140 bL31m 1 AT5G55125 AT1G27435 bL33m AT5G18790 bL36m AT5G20180 mL40 AT4G05400 mL41 1 AT5G40080 AT5G39800 mL43 AT3G59650 mL46 AT1G14620 mL53 AT5G39600 mL54 AT3G01740 mL101 (rPPR4 3 ) AT1G60770 mL102 (rPPR5 3 ) AT2G37230 mL103 (rPPR7 3 ) AT4G36680 mL104...”
• QTL and Transcriptomic Analyses Implicate Cuticle Transcription Factor SHINE as a Source of Natural Variation for Epidermal Traits in Cucumber Fruit
  Rett-Cadman, Frontiers in plant science 2019
  • “...18.5 7.2 11 unknown At1g52565 2.1 e12 CsaV31g030220 124.2 99.5 86.7 99.8 50S ribosomal L36 At5g20180 2.3e30 CsaV31g030230 28.4 21.7 40.8 30.7 DUF 4050 family protein At5g25360 2.5e58 CsaV31g030250 0.1 0.5 0.5 0.1 EIN3 binding F-box protein-like At5g25350 1.8e84 CsaV31g030300 175.0 128.5 100.7 106.2 tetratricopeptide repeat...”

4v61B6 4v61B6 (see paper)
63% identity, 100% coverage

• Ligand: rna (4v61B6)

HPG27_RS06525 50S ribosomal protein L36 from Helicobacter pylori
71% identity, 100% coverage

• Insight into the essential role of the Helicobacter pylori HP1043 orphan response regulator: genome-wide identification and characterization of the DNA-binding sites
  Pelliciari, Scientific reports 2017
  • “...genome amplified by PCR with oligonucleotides 1296FPF/1296FPR. This region encompasses the putative promoter region of HPG27_RS06525 (HP1297 according to 26695 annotation). This work pGEMp1260 pGEM-T-Easy derivative, containing a 242bp DNA fragment corresponding to the region from 1.321.773 to 1.322.015 of H. pylori G27 genome amplified by...”

LSEI_2480 Ribosomal protein L36 from Lactobacillus casei ATCC 334
61% identity, 100% coverage

• Physiological and transcriptional response of Lactobacillus casei ATCC 334 to acid stress
  Broadbent, Journal of bacteriology 2010
  • “...LSEI_2272 LSEI_2273 LSEI_2476 LSEI_2478 LSEI_2479 LSEI_2480 LSEI_2481 LSEI_2484 LSEI_2485 LSEI_2486 LSEI_2487 LSEI_2488 LSEI_2489 LSEI_2490 LSEI_2491 LSEI_2492...”

NMB0164 50S ribosomal protein L36 from Neisseria meningitidis MC58
NMA0107 50S ribosomal protein L36 from Neisseria meningitidis Z2491
76% identity, 100% coverage

• The zinc-responsive regulon of Neisseria meningitidis comprises 17 genes under control of a Zur element
  Pawlik, Journal of bacteriology 2012
  • “...L31 and L36 are NMB1956 (C)/ NMB0942 (C) and NMB0164 (C)/NMB0941 (C), respectively (34, 51). The nmb0942-nmb0941 (rpmEJ) operon was shown to be repressed at...”
• Transcriptome analysis of Neisseria meningitidis during infection
  Dietrich, Journal of bacteriology 2003
  • “...NMB0149 NMB0150 NMB0151 NMB0159 NMB0160 NMB0161 NMB0163 NMB0164 NMB0167 NMB0169 NMB0941 NMB0942 NMB0232 NMB0987 NMB0961 NMB0091 NMB0092 NMB0093 NMB0200 NMB0267...”
• Analysis of the heat shock response of Neisseria meningitidis with cDNA- and oligonucleotide-based DNA microarrays
  Guckenberger, Journal of bacteriology 2002
  • “...NMB0554 NMB0712 NMB0791 NMB1366 NMB1538 NMB1972 NMB1973 NMB0164 NMB0165 NMB0214 NMB0294 NMB0370 NMB0557 NMB0561 NMB0604 NMB0906 NMB0907 NMB0946 NMB0947 NMB1056...”
• Transcriptome analysis of Neisseria meningitidis during infection
  Dietrich, Journal of bacteriology 2003
  • “...NMA0122 NMA0121 NMA0120 NMA0112 NMA0111 NMA0110 NMA0108 NMA0107 NMA0104 NMA0102 NMA1137 NMA1138 NMA0027 NMA1303/NMA1188 Absent Absent Absent Absent Absent...”

sml0006 50S ribosomal protein L36 from Synechocystis sp. PCC 6803
63% identity, 100% coverage

• Small proteins in cyanobacteria provide a paradigm for the functional analysis of the bacterial micro-proteome
  Baumgartner, BMC microbiology 2016
  • “...Y 32865 32978 - 37 ssl5031 NA NA Y N N 831101 831217 - 38 sml0006 rpl36 50S ribosomal protein L36 Y Y Y| 1823570 1823686 + 38 smr0010 petG Cytochrome b 6 f complex subunit 5 Y Y N 2350140 2350256 - 38 sml0001 psbI...”
• Expression profiling of the bloom-forming cyanobacterium Nodularia CCY9414 under light and oxidative stress conditions
  Kopf, The ISME journal 2015
  • “...107) Slr1909 (e 109) Slr0338 (0.0) Slr2025 (e 37) None Sml0006 (e 17) Slr1834HL (0.0) Sll0990 (e 13) None None Sll1932 (0.0) Slr0354 (e 101) None None Slr2070...”
• Gene expression patterns of sulfur starvation in Synechocystis sp. PCC 6803
  Zhang, BMC genomics 2008
  • “...complex slr1185( petC ), slr1828( petF ), Ribosomal proteins (sll1816( rps13 ), slr1984( rps1 ), sml0006( rpl36 ), ssl3437( rps17 ), ssl3445( rpl31 ), ssr0482( rps16 )) 20 slr2075( groES ), Ribosomal proteins (sll1824, slr0628( rps14 ), ssl2233( rps20 )) The differentially expressed genes in Synechocystis...”

SPy0076 50S ribosomal protein B from Streptococcus pyogenes M1 GAS
66% identity, 100% coverage

• Global Analysis and Comparison of the Transcriptomes and Proteomes of Group A Streptococcus Biofilms
  Freiberg, mSystems 2016
  • “...Late biofilm Versus early log phase Versus late log phase Versus early stationary phase Upregulated Spy0076 rpmJ 1.98 1.63 1.56 1.45 1.67 1.33 1.25 50S ribosomal protein L36 I Spy0446 1.55 1.07 1.37 1.81 1.33 1.63 1.24 1.06 Serine kinase; regulates carbohydrate metabolism T A Spy0447...”

Dde_2235 50S ribosomal protein L36 from Oleidesulfovibrio alaskensis G20
Dde_2235 Ribosomal protein L36 from Desulfovibrio desulfuricans G20
68% identity, 100% coverage

• Transcriptome-wide marker gene expression analysis of stress-responsive sulfate-reducing bacteria
  Jawaharraj, Scientific reports 2023
  • “...regulatory protein P-II Dde_2819 4.23 1.02 Uncharacterized protein Dde_2375 3.66 1.47 Heavy metal-binding domain-containing protein Dde_2235 3.48 1.62 50S ribosomal protein L36 Dde_3449 3.45 1.68 4Fe-4S ferredoxin-type domain-containing protein Dde_3226 3.37 0.21 Phage shock protein A, PspA Dde_0814 3.32 1.66 Uncharacterized protein Dde_3071 3.21 1.50 Polar...”

7nhk8 / A0A1B4XKT9 7nhk8 (see paper)
Q839E1 Large ribosomal subunit protein bL36 from Enterococcus faecalis (strain ATCC 700802 / V583)
IUJ47_RS04640 50S ribosomal protein L36 from Enterococcus faecalis
63% identity, 100% coverage

• Ligands: rna; zinc ion (7nhk8)
• 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
  • “...family 22.21 17.94 0.81 Q833B0 EF_2057 Heptaprenyl diphosphate synthase, component II, putative 23.11 18.59 0.80 Q839E1 rpmJ 50S ribosomal protein L36 22.37 17.89 0.80 Q834B0 EF_1759 Phosphate-binding protein 24.43 19.32 0.79 Q832R8 EF_2150 Aminoacyltransferase FemA 20.95 16.23 0.77 Q834N1 pflB Formate acetyltransferase 20.93 15.78 0.75 Q839C0...”
• Gliotoxin-mediated bacterial growth inhibition is caused by specific metal ion depletion
  Downes, Scientific reports 2023
  • “...Isopentenyl-diphosphate delta-isomerase Unique N/A 4 15 Q837E2 50S ribosomal protein L36* Unique N/A 2 60.5 Q839E1 ABC transporter, ATP-binding protein* Unique N/A 7 47 Q839U4 Dihydropteroate synthase* Unique N/A 4 20.9 Q82Z14 CBS domain protein* Unique N/A 8 54.7 Q830P4 4-hydroxy-tetrahydrodipicolinate synthase* Unique N/A 10 54.5...”
• Antibacterial Components and Modes of the Methanol-Phase Extract from Commelina communis Linn
  Liu, Plants (Basel, Switzerland) 2023
  • “...ribosomal protein L11 IUJ47_RS01030 0.185 50S ribosomal protein L1 IUJ47_RS04565 0.189 50S ribosomal protein L29 IUJ47_RS04640 0.195 50S ribosomal protein L36 IUJ47_RS04530 0.201 50S ribosomal protein L4 IUJ47_RS07500 0.222 50S ribosomal protein L35 IUJ47_RS01420 0.226 50S ribosomal protein L33 IUJ47_RS04645 0.229 30S ribosomal protein S13 IUJ47_RS04540...”

CNAG_01974 large subunit ribosomal protein L36 from Cryptococcus neoformans var. grubii H99
61% identity, 36% coverage

• Ubiquitin Degradation of the AICAR Transformylase/IMP Cyclohydrolase Ade16 Regulates the Sexual Reproduction of Cryptococcus neoformans
  Han, Journal of fungi (Basel, Switzerland) 2023
  • “.... Accession Description Average fbp1 /H99 No. of PEST Domain CNAG_05514 Uncharacterized protein 1.899038 0 CNAG_01974 Ribosomal protein 1.631707 2 CNAG_06195 Uncharacterized protein 1.595274 0 CNAG_00700 ATIC Ade16 1.544354 0 CNAG_05498 Uncharacterized protein 1.541769 1 CNAG_02860 Endo-1,3(4)-beta-glucanase 1.522101 2 CNAG_01019 Superoxide dismutase 1.470508 0 CNAG_02344 Uracil...”

Q04BZ2 Large ribosomal subunit protein bL36 from Lactobacillus delbrueckii subsp. bulgaricus (strain ATCC BAA-365 / Lb-18)
63% identity, 100% coverage

• Effects of ccpA gene deficiency in Lactobacillus delbrueckii subsp. bulgaricus under aerobic conditions as assessed by proteomic analysis
  Zhang, Microbial cell factories 2020
  • “...30S ribosomal protein S17 10.49 45.45 1.542 G6EVN1 50S ribosomal protein L4 21.87 43.72 1.529 Q04BZ2 50S ribosomal protein L36 4.41 26.32 1.517 Q1G7Z4 tRNA modification GTPase MnmE 49.93 32.32 1.510 Q1G905 50S ribosomal protein L12 12.34 59.50 1.506 F0HW20 50S ribosomal protein L34 5.41 13.04...”

I872_00600 50S ribosomal protein L36 from Streptococcus cristatus AS 1.3089
llmg_2357 50S ribosomal protein L36 from Lactococcus lactis subsp. cremoris MG1363
SSUSC84_0092 50S ribosomal protein L36 from Streptococcus suis SC84
63% identity, 100% coverage

• Redox-Regulated Adaptation of Streptococcus oligofermentans to Hydrogen Peroxide Stress
  Tong, mSystems 2020
  • “...0 36.5 3.5* 10 I872_03205 Thioredoxin family protein FWASWCGPCK b C82 10 80 100 11 I872_00600 50S ribosomal protein L36 VMVICPANPK C27 100 24 6 100* a The thiol/disulfide oxidized ratio was calculated by dividing the intensity of oxidized disulfide-linked peptide by the sum of the...”
• Disruption of a Transcriptional Repressor by an Insertion Sequence Element Integration Leads to Activation of a Novel Silent Cellobiose Transporter in Lactococcus lactis MG1363
  Solopova, Applied and environmental microbiology 2017
  • “...protein llmg_2356 llmg_2356 ribosomal protein -6.8 -9.1 llmg_2357 llmg_2357 ribosomal protein -8.4 -9.2 llmg_2374 llmg_2374 ribosomal protein -6.4 -6.6...”
• Exogenous glycogen utilization effects the transcriptome and pathogenicity of Streptococcus suis serotype 2
  Tan, Frontiers in cellular and infection microbiology 2022
  • “...change of RNA-Seq Fold change of qRT-PCR SSUSC84_0015 ftsH ATP-dependent zinc metalloprotease -3.45 -4.76 1.03 SSUSC84_0092 rpmJ 50S ribosomal protein L36 -7.14 -12.50 1.40 SSUSC84_0249 adhP Alcohol dehydrogenase 76.28 61.15 3.51 SSUSC84_0270 dnaJ Molecular chaperone 7.58 2.84 0.65 SSUSC84_0376 cysK Cysteine synthase A -6.25 -5.88 1.12...”

YSS_RS00895 50S ribosomal protein L36 from Campylobacter coli RM4661
63% identity, 100% coverage

• Proteotyping as alternate typing method to differentiate Campylobacter coli clades
  Emele, Scientific reports 2019
  • “...scheme. ORF No. (RM4661) Gene product Forward primer (53) Reverse primer (53) Amplicon length [bp] YSS_RS00895 RpmJ/L36 AGCTGCTGCTTCATCTTCACT AGCCTTGATAAAGGGCGTATC 490 YSS_RS04330 RpmH/L34 AAATGCTCGGGCAAATTGATTA GCCATCGCAATACCACTTTT 512 YSS_RS01420 RpmF/L32 TGCACCACTATGTCCTGCTG TGCCACAATGCAAGGTTTTGT 728 YSS_RS02145 RpmG/L33 AGCTGATGGCGTTGAAATGG ACCCCCAACCATCGGATTTG 430 YSS_RS09385 RpsN/S14 ACACGACGACCTGGTTTAGA TCGGTCTTGATGAGCAGTTGA 611 YSS_RS09410 RpmC/L29 GGTCTGCATTCAACCGCTAC GCCAAATTGAAGCAGCTCGT 668 YSS_RS02020...”

7ood2 / P52864 Mycoplasma pneumoniae 50s subunit of ribosomes in chloramphenicol- treated cells (see paper)
71% identity, 100% coverage

• Ligands: rna; zinc ion (7ood2)

EKO22_07880 50S ribosomal protein L36 from Synechococcus elongatus PCC 11802
66% identity, 100% coverage

• A Novel Cyanobacterium Synechococcus elongatus PCC 11802 has Distinct Genomic and Metabolomic Characteristics Compared to its Neighbor PCC 11801
  Jaiswal, Scientific reports 2020
  • “...survival under prolonged exposure to antibiotics by entering a dormant state 82 YoeB toxin protein EKO22_07880 QFZ92285 Proteins unique to PCC 11801 Putative ski2-type helicase MJ1124 DOP62_06670 AZB72445 RNA degradation, processing, and splicing Demonstrated to activate RNA degradation in eukaryotes 83 HigA protein (antitoxin to HigB)...”

RL36_THET8 / Q5SHR2 Large ribosomal subunit protein bL36; 50S ribosomal protein L36; Ribosomal protein B from Thermus thermophilus (strain ATCC 27634 / DSM 579 / HB8) (see paper)
RL36_THETH / P80256 Large ribosomal subunit protein bL36; 50S ribosomal protein L36; Ribosomal protein B from Thermus thermophilus (see paper)
68% identity, 100% coverage

• cofactor: Zn(2+) (Binds 1 zinc ion per subunit.)
  subunit: Part of the 50S ribosomal subunit
• cofactor: Zn(2+) (Binds 1 zinc ion per subunit.)
  subunit: Part of the 50S ribosomal subunit

A5IV11 Large ribosomal subunit protein bL36 from Staphylococcus aureus (strain JH9)
Q2FW29 Large ribosomal subunit protein bL36 from Staphylococcus aureus (strain NCTC 8325 / PS 47)
SAS078 50S ribosomal protein L36 from Staphylococcus aureus subsp. aureus N315
SAOUHSC_02488 ribosomal protein L36 from Staphylococcus aureus subsp. aureus NCTC 8325
USA300HOU_2218 ribosomal protein L36 from Staphylococcus aureus subsp. aureus USA300_TCH1516
SACOL2216 ribosomal protein L36 from Staphylococcus aureus subsp. aureus COL
ACIV1F_002546, B4602_RS11710, EKM74_RS05515 50S ribosomal protein L36 from Staphylococcus aureus
68% identity, 100% coverage

• A Carvacrol-Rich Essential Oil Extracted From Oregano (Origanum vulgare "Hot & Spicy") Exerts Potent Antibacterial Effects Against Staphylococcus aureus
  Hao, Frontiers in microbiology 2021
  • “...Table 3 . DEPs with an fold change (FC) value of more than 2 included A5IV11 (50S ribosomal protein L36), A0A380DL04 (ribitol-5-phosphate cytidylyltransferase), A0A380DI91 (ribokinase), A0A033UKY8 (50S ribosomal protein L7/L12), A0A0D1EWN0 (phosphoribosylformylglycinamidine synthase subunit PurS), A5IPU8 (30S ribosomal protein S18), A8Z216 (50S ribosomal protein L33 2),...”
  • “...polymerase subunit omega A5ITD6 0.56 0.036 Down Uridine kinase A5ITM2 1.57 0.033 Up ATP-dependent 6-phosphofructokinase A5IV11 5.36 0.015 Up 50S ribosomal protein L36 A5IV16 1.97 0.001 Up 50S ribosomal protein L30 A7 0P6 0.64 0.034 Down UDP- N -acetylmuramoyl- L -alanyl- D -glutamate L -lysine ligase...”
• Molecular physiological characterization of the dynamics of persister formation in <i>Staphylococcus aureus</i>
  Liu, Antimicrobial agents and chemotherapy 2024 (secret)
• Antibacterial Activity of Juglone against Staphylococcus aureus: From Apparent to Proteomic
  Wang, International journal of molecular sciences 2016
  • “...0.603 0.008 Protein synthesis Q2FW17 50s ribosomal protein l24 rplX 2 2 11.50 1.225 0.001 Q2FW29 50s ribosomal protein l36 rpmJ 1 1 4.30 0.704 0.002 Q2FW16 50s ribosomal protein l14 rplN 4 4 13.10 0.734 0.010 Q2FY22 50S ribosomal protein L33 2 rpmG2 1 1...”
• 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
  • “...gene Primers used for cloning of antisense products rpmJ (SAS078) SAR1012 rpmC (SA2039) rpsT (SA1414) hup (SA1305) Primers used for PCR and sequencing of genes...”
  • “...PSM3 PSM3 Delta-toxin Delta-toxin SA2420.1 SA2420.1 rpmJ (SAS078) SAR1012 SAR1012 SAR1012 graF (SAS030) graF (SAS030) graF (SAS030) SAS049 SAS049 SAS049 SAS049...”
• Transcriptional profiles of the response of methicillin-resistant Staphylococcus aureus to pentacyclic triterpenoids
  Chung, PloS one 2013
  • “...rpmH 50S ribosomal protein L34 6.3 Translation SA1503 rpmI 50S ribosomal protein L35 6.0 Translation SAS078 rpmJ 50S ribosomal protein L36 21.0 Translation SA2035 rplE 50S ribosomal protein L5 6.3 Translation SA0498 rplL 50S ribosomal protein L7/L12 8.3 Translation SA0014 rplI 50S ribosomal protein L9 2.8...”
• Antibacterial Components and Modes of the Methanol-Phase Extract from Commelina communis Linn
  Liu, Plants (Basel, Switzerland) 2023
  • “...0.383 Conserved hypothetical protein SAOUHSC_02495 0.384 Ribosomal protein L18 SAOUHSC_02496 0.389 Ribosomal protein L6 putative SAOUHSC_02488 0.391 Ribosomal protein L36 SAOUHSC_02486 0.400 Ribosomal protein S11 putative SAOUHSC_02501 0.409 Ribosomal protein L24 SAOUHSC_02502 0.413 Ribosomal protein L14 SAOUHSC_02500 0.416 50S ribosomal protein L5 putative SAOUHSC_00017 0.419 Ribosomal...”
• Increased mutability of Staphylococci in biofilms as a consequence of oxidative stress
  Ryder, PloS one 2012
  • “...Accessory gene regulator protein C 2.62 up SAOUHSC_02350 atpB ATP synthase subunit A 2.03 up SAOUHSC_02488 rpmJ 50S ribosomal protein L36 2.23 up 144 hr Biofilms/Planktonic SAOUHSC_01683 dnaK Chaperone protein DnaK 2.17 up SAOUHSC_01684 grpE Protein GrpE 2.47 up SAOUHSC_01685 hrcA Heat-inducible transcription repressor HrcA 2.43...”
• Protein S-Bacillithiolation Functions in Thiol Protection and Redox Regulation of the Glyceraldehyde-3-Phosphate Dehydrogenase Gap in Staphylococcus aureus Under Hypochlorite Stress
  Imber, Antioxidants & redox signaling 2018
  • “...0.04 USA300HOU_1553 rpmG3 Ribosomal protein L33 Cys36 a B 6.6 9.46 5.76 0.10 15.22 0.12 USA300HOU_2218 rpmJ Ribosomal protein L36 Cys11 a (-SSB) B 4.5 16.93 21.38 0.17 38.32 0.11 USA300HOU_2218 rpmJ Ribosomal protein L36 Cys27 a B 3.1 16.52 6.69 0.43 23.21 0.10 Transport and...”
  • “...switches are the Zn-containing alcohol dehydrogenase Adh (USA300HOU_0610), the ribosomal proteins RpmG3 (USA300HOU_1553), and RpmJ (USA300HOU_2218). Zn-containing ribosomal proteins share three to four Cys residues that are suggested to serve as reservoir for Zn storage ( 54 ). As another Zn redox switch, we identified the...”
• Copper stress induces a global stress response in Staphylococcus aureus and represses sae and agr expression and biofilm formation
  Baker, Applied and environmental microbiology 2010
  • “...SACOL0591 SACOL0592 SACOL0593 SACOL2212 SACOL2213 SACOL2216 SACOL2217 SACOL2220 SACOL2224 SACOL2225 SACOL2226 SACOL2227 SACOL2228 SACOL2229 SAV2247 SACOL2234...”
• Response of <i>Staphylococcus aureus</i> to combination of virulent bacteriophage vB_SauM-515A1 and linezolid
  Abdraimova, Frontiers in microbiology 2024
  • “...et al., 2020 ). During combined treatment, transcription of genes encoding both large (ACIV1F_000615; ACIV1F_001627; ACIV1F_002546; ACIV1F_002564) and small (ACIV1F_001630; ACIV1F_002560; ACIV1F_002565) ribosomal subunit proteins also changed, though the GO term for translation was not significantly enriched. Additionally, following 30 min of antibiotic exposure, there was...”
• Combined proteomic and transcriptomic analysis of the antimicrobial mechanism of tannic acid against Staphylococcus aureus
  Wang, Frontiers in pharmacology 2023
  • “...50S ribosomal protein L16 1.62 0.48 B4602_RS11810 rplB WP_000985472.1 50S ribosomal protein L2 1.86 0.96 B4602_RS11710 rpmJ WP_000868342.1 50S ribosomal protein L36 0.85 2.7 B4602_RS06750 rpsN WP_001085655.1 30S ribosomal protein S14 2.56 3.16 B4602_RS11660 rpsI WP_001790547.1 30S ribosomal protein S9 0.99 1.25 B4602_RS01735 rpsR WP_000897044.1 30S...”
• Transcriptomic Analysis Revealed Antimicrobial Mechanisms of Lactobacillus rhamnosus SCB0119 against Escherichia coli and Staphylococcus aureus
  Peng, International journal of molecular sciences 2022
  • “...ribosomal protein S11 EKM74_RS05510 582.25 5.82 10,572.69 1079.55 4.182553 rpsM ; 30S ribosomal protein S13 EKM74_RS05515 259.55 26.92 8724.69 798.78 5.071017 rpmJ ; 50S ribosomal protein L36 EKM74_RS05535 328.44 51.85 2770.35 239.31 3.076378 rplO ; 50S ribosomal protein L15 EKM74_RS05540 370.08 105.31 13,564.79 1089.74 5.195877 rpmD...”

B3DFA8 Large ribosomal subunit protein bL36 from Microcystis aeruginosa (strain NIES-843 / IAM M-2473)
63% identity, 100% coverage

• Rapid Classification and Identification of Microcystis aeruginosa Strains Using MALDI-TOF MS and Polygenetic Analysis
  Sun, PloS one 2016 (no snippet)

TP0209 ribosomal protein L36 (rpmJ-1) from Treponema pallidum subsp. pallidum str. Nichols
TPANIC_RS01040 50S ribosomal protein L36 from Treponema pallidum subsp. pallidum str. Nichols
63% identity, 100% coverage

• The protein network of bacterial motility
  Rajagopala, Molecular systems biology 2007
  • “...motility phenotype and their interactions with other motility proteins. Among these proteins, ribosomal protein RpmJ/L36 (TP0209) is an unexpected case, because it not only interacted with multiple flagellar proteins, but also showed a reduction of motility to about 14% of the wild type when mutated. It...”
  • “...rapG (BSU), HP1479 (HPY) FliM Schumann et al (2001) ; Salama et al (2004) COG0267 TP0209 rpmJ (ECO) FliG-2, CheR, FliY, FlgE, FliS /+ a COG1774 TP0046 yaaT (BSU) CheR,FlgD, MetK, FlaB3, TP0959, CheW-2,Mcp2-3 /+ Schumann et al (2001) COG0084 TP0979 ycfH ( tatD ) (ECO)...”
• Transcriptome of Treponema pallidum: gene expression profile during experimental rabbit infection
  Smajs, Journal of bacteriology 2005
  • “...TP0609 TP0888 TP0848 TP0115 TP0488 TP0486 TP0298 TP0939 TP0363 TP0823 TP0209 TP0237 TP0244 TP0850 TP0361 TP1041 5.2 5.1 5.1 5.0 4.8 4.7 4.6 4.6 4.5 4.5 4.4 4.3...”
• Comparison of transcriptional profiles of Treponema pallidum during experimental infection of rabbits and in vitro culture: Highly similar, yet different
  De, PLoS pathogens 2021
  • “.../ gluconeogenesis 2,741 8,436 1.62 .0002 TPANIC_0869 hypothetical protein Hypothetical protein 69 232 1.64 6.10E-12 TPANIC_RS01040 rpmJ Translation; Ribosomal proteins: Synthesis and modification 7 25 1.69 .001 TPANIC_0163 troA Transport and binding proteins; Cations 388 1,210 1.70 1.04E-12 TPANIC_0856 UPF0164 family protein Other categories; Unknown* 1,266...”

MSMEG_1520 ribosomal protein L36 from Mycobacterium smegmatis str. MC2 155
68% identity, 100% coverage

• Monitoring global protein thiol-oxidation and protein S-mycothiolation in Mycobacterium smegmatis under hypochlorite stress
  Hillion, Scientific reports 2017
  • “...rpsN 30S ribosomal protein S14 type Z 27* B 19,6 41,5 60,1 13,0 32,5 45,5 MSMEG_1520 rpmJ 50S ribosomal protein L36 27* B 33,5 21,7 43,6 13,5 22,4 35,9 MSMEG_1521 rpsM 30S ribosomal protein S13 86* (MSH;Cys) B 21,8 10,4 32,9 20,2 14,7 34,4 MSMEG_1579 rimI...”
• Gene Expression, Bacteria Viability and Survivability Following Spray Drying of Mycobacterium smegmatis
  Lauten, Materials (Basel, Switzerland) 2010
  • “...L34 rpmH 0.3 11.5 0.282 0% MSMEG_3792 ribosomal protein L35 rpmI 0.8 13.6 0.004 46% MSMEG_1520 ribosomal protein L36 rpmJ 0.4 13.3 0.080 1% MSMEG_3833 ribosomal protein S1 -0.3 12.1 0.174 1% MSMEG_2519 ribosomal protein S2 rpsB 2.0 11.7 0.000 100% MSMEG_1442 ribosomal protein S3 rpsC...”

MT3567.1 50S ribosomal protein L36 from Mycobacterium tuberculosis CDC1551
Rv3461c 50S ribosomal protein L36 from Mycobacterium tuberculosis H37Rv
68% identity, 100% coverage

• 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
  • “...MT0728, MT0747, MT1337, MT2117.1, MT0663, MT4041.1, MT1680, MT3567.1, MT0729, MT0742, MT0744, MT0681, MT0062 Small subunit 22 MT1666, MT0727, MT3566, MT0710,...”
• Bedquiline Resistance Mutations: Correlations with Drug Exposures and Impact on the Proteome in M. tuberculosis
  Xu, Antimicrobial agents and chemotherapy 2023
  • “...mIHF 2.0 2.2 1.8 1.9 Rv0979A rpmF 50S ribosomal protein L32 2.0 3.8 2.4 2.7 Rv3461c rpmJ 50S 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...”
• Modeling Site-Specific Nucleotide Biases Affecting Himar1 Transposon Insertion Frequencies in TnSeq Data Sets
  Choudhery, mSystems 2021
  • “...the TTN-Fitness method (mostly as Non-Essential [51 genes] or Growth-Defect [18 genes]) ( Fig.11B ). Rv3461c ( rpmJ , 50S ribosomal protein L36), a gene with 3 TA sites, is an example of such an Uncertain gene ( 8 ). The gene is seen in Fig.12B...”
  • “...gene is similar to other genes labeled Growth Defect or Essential by the HMM+NP model. Rv3461c is a part of the L3P family of ribosomal proteins. Other genes in this family have been labeled as Essential or Growth Defect by the HMM+NP model and Growth Defect...”
• Hypoxia Is Not a Main Stress When Mycobacterium tuberculosis Is in a Dormancy-Like Long-Chain Fatty Acid Environment
  Del, Frontiers in cellular and infection microbiology 2018
  • “...L-lysine aminotransferase Rv3417c groEL 1.13E-15 2.66E-05 Molecular chaperone GroEL Rv3418c groES 4.60E-13 2.36E-57 Co-chaperonin GroES Rv3461c rpmJ 5.00E-03 8.32E-04 50S ribosomal protein L36 Rv3679 1.13E-11 2.38E-10 Anion transporter ATPase Rv3872 PE35 2.50E-05 4.88E-07 PE family-like protein DE, dextrose exponential; DNRP1, dextrose early hypoxia; DNRP2, dextrose late...”
• Mycobacterium tuberculosis septum site determining protein, Ssd encoded by rv3660c, promotes filamentation and elicits an alternative metabolic and dormancy stress response
  England, BMC microbiology 2011
  • “...rpsD -0.8 -0.5 Rv3561 fadD3 0.8 0.5 Rv3460c rpsM -1.3 -0.6 Rv0035 fadD34 1.3 0.0 Rv3461c rpmJ -1.4 -0.6 Rv0214 fadD4 0.8 -0.2 Rv3924c rpmH -1.2 -0.7 Rv0551c fadD8 0.9 0.0 Rv2590 fadD9 1.3 -0.5 Anaerobic respiration Rv0972c fadE12 1.4 -0.1 Rv0252 nirB 0.8 ndr Rv0975c...”
• Sequence-based analysis uncovers an abundance of non-coding RNA in the total transcriptome of Mycobacterium tuberculosis
  Arnvig, PLoS pathogens 2011
  • “...rpoZ II.A.7 287 Rv3615c espC V 284 Rv1793 esxN VI 271 Rv1626 two-comp I.J.2 271 Rv3461c rpmJ II.A.1 247 Rv3153 nuoI I.B.6a 246 Rv0250c CHP V 244 Rv3678A CHP I.J.1 232 Rv2840c CHP V 230 Rv0700 rpsJ II.A.1 224 Rv1630 rpsA II.A.1 220 Rv2472 CHP V...”
• The gene expression data of Mycobacterium tuberculosis based on Affymetrix gene chips provide insight into regulatory and hypothetical genes
  Fu, BMC microbiology 2007
  • “...fbpA 6875 410 Rv0440 groEL2 3650 935 Rv0703 rplW 6378 651 Rv0668 rpoC 3637 661 Rv3461c rpmJ 6349 379 Rv3849 - 3615 650 Rv1298 rpmE 6160 765 Rv1211 - 3606 386 Rv3418c groES 6017 1376 Rv2204c - 3605 594 Rv1177 fdxC 6004 569 Rv1310 atpD 3604...”
• Quantification of global transcription patterns in prokaryotes using spotted microarrays
  Sidders, Genome biology 2007
  • “...2,195 Unknown 39 Rv3763 lpqH 2,180 Lipoproteins (lppA-lpr0) 40 Rv1872c lldD2 2,149 Aerobic respiration 41 Rv3461c rpmJ 2,133 Ribosomal protein synthesis* 42 Rv1361c PPE19 2,127 PPE family 43 Rv0097 Rv0097 2,123 Conserved hypotheticals 44 Rv1971 Rv1971 2,034 Virulence 45 Rv3051c nrdE 1,984 2'-Deoxyribonucleotide metabolism* 46 Rv2346c...”
  • “...In vitro 21 Rv1072 Rv1072 1,897 560 - 22 Rv1872c lldD2 1,817 574 - 23 Rv3461c rpmJ 1,814 795 In vitro 24 Rv2457c clpX 1,790 343 In vitro 25 Rv0700 rpsJ 1,693 1,148 In vitro 26 Rv1078 pra 1,643 971 - 27 Rv1298 rpmE 1,529 543...”

CAC3108 Ribosomal protein L36 from Clostridium acetobutylicum ATCC 824
CD0094A 50S ribosomal protein L36 from Clostridium difficile 630
66% identity, 100% coverage

• Transcriptional organization of the Clostridium acetobutylicum genome
  Paredes, Nucleic acids research 2004
  • “...contains 28 genes starting at CAC3135 and ending at CAC3108, and among them, 23 encode ribosomal proteins. Another long TU contains 22 genes (from CAC1365 to...”
• Semiquantitative analysis of clinical heat stress in Clostridium difficile strain 630 using a GeLC/MS workflow with emPAI quantitation
  Ternan, PloS one 2014
  • “...( Figure 4 ) encompassing L3L15 (CD0073, rplC CD0089, rplO ), secY L36 (CD0090, prlA CD0094A, rpmJ ), S13 S4 (CD0095, rpsM CD0097, rpsD ) and DNA directed RNA polymerase subunit (CD0098, rpoA ). Thus the transcriptional arrangement as predicted for C. difficile is quite different...”

9c4g3 / A0A2B7JN22 Cutibacterium acnes 50s ribosomal subunit with clindamycin bound (see paper)
66% identity, 100% coverage

• Ligand: rna (9c4g3)

RL36_BACSU / P20278 Large ribosomal subunit protein bL36; 50S ribosomal protein L36; BL38; Ribosomal protein B; Ribosomal protein II from Bacillus subtilis (strain 168) (see paper)
7as8j / P20278 Bacillus subtilis ribosome quality control complex state b. Ribosomal 50s subunit with p-tRNA, rqch, and rqcp/yabo (see paper)
BSU01400 50S ribosomal protein L36 from Bacillus subtilis subsp. subtilis str. 168
63% identity, 100% coverage

• subunit: Part of the 50S ribosomal subunit.
• Ligand: rna (7as8j)
• The Blueprint of a Minimal Cell: MiniBacillus
  Reuß, Microbiology and molecular biology reviews : MMBR 2016
  • “...BSU37070 BSU15080 BSU24900 BSU00990 BSU41060 BSU28860 BSU01400 BSU16490 BSU01220 BSU29660 BSU01330 BSU40910 BSU01110 BSU01300 BSU01500 BSU01150 BSU01420...”

SCO4726 50S ribosomal protein L36 from Streptomyces coelicolor A3(2)
63% identity, 100% coverage

• System-Wide Analysis of the GATC-Binding Nucleoid-Associated Protein Gbn and Its Impact on Streptomyces Development
  Du, mSystems 2022
  • “...0.24 SCO4721 RplO (50S ribosomal protein L15) 380 432 +22 +21 34.82 29.13 0.23 0.18 SCO4726 RpmJ (50S ribosomal protein L36) 310 761 3 +21 6.69 15.32 0.02 0.07 SCO4727 RpsM (30S ribosomal protein S13) 305 282 0.05 0.16 SCO5880 b RedY (RedY protein) 286 347...”
• Correcting for link loss in causal network inference caused by regulator interference
  Wang, Bioinformatics (Oxford, England) 2014
  • “...criteria showed that five predicted targets were significantly altered at the 0.5% level (SCO1196, SCO3899, SCO4726, SCO5390, SCO6753), and three others at 5% ( Supplementary Table S3 ). The second criteria indicated that five targets (SCO3899, SCO4545, SCO4653, SCO4726, SCO6753) and the operon (seven genes) have...”
• A novel two-component system involved in the transition to secondary metabolism in Streptomyces coelicolor
  Rozas, PloS one 2012
  • “...RpsH, 30S ribosomal protein S8 SCO4719 2.04 2.34 SCO4701-4721 * RpsE, 30S ribosomal protein S5 SCO4726 2.04 2.14 SCO4724-4731 * RpmJ, 50S ribosomal protein L36 SCO4956 2.02 2.31 SCO4956 Possible peptide methionine sulfoxide reductase SCO5999 2.63 2.75 SCO5999 Hypothetical protein Secretory proteins SCO6109 2.18 2.19 SCO6108-6109...”
• Metabolic switches and adaptations deduced from the proteomes of Streptomyces coelicolor wild type and phoP mutant grown in batch culture
  Thomas, Molecular & cellular proteomics : MCP 2012
  • “...(SCO3672) pH units and molecular masses from 4.4 kDa (SCO4726, 50 S ribosomal protein L36) to 799 kDa (SCO3230, CDA PS1), implying a good coverage of physical...”
• Comparative genomics of Streptomyces avermitilis, Streptomyces cattleya, Streptomyces maritimus and Kitasatospora aureofaciens using a Streptomyces coelicolor microarray system
  Hsiao, Antonie van Leeuwenhoek 2008
  • “...protein L30 0.13 0.39 0.64 0.26 SCO4721 50S ribosomal protein L15 1.79 0.42 0.80 0.84 SCO4726 50S ribosomal protein L36 0.46 0.13 0.35 0.10 SCO4727 30S ribosomal protein S13 0.63 0.23 0.62 0.17 SCO4728 30S ribosomal protein S11 1.12 0.55 0.87 0.27 SCO4730 50S ribosomal protein...”
• Zinc-responsive regulation of alternative ribosomal protein genes in Streptomyces coelicolor involves zur and sigmaR
  Owen, Journal of bacteriology 2007
  • “...L33 rpmF1 (SCO5571) rpmG1 (SCO4635) L36 rpmJ1 (SCO4726) rpsN2 (SCO3430) rpsR2 (SCO3425) rpmB2 (SCO3429) rpmE2 (SCO3427) rpmE3 (SCO1150) rpmF2 (SCO0436) rpmG2...”
• The global role of ppGpp synthesis in morphological differentiation and antibiotic production in Streptomyces coelicolor A3(2)
  Hesketh, Genome biology 2007
  • “...) is predicted to encode an alternative form of the L36 ribosomal protein specified by SCO4726 ( rpmJ1 ). The major difference between the two forms is that SCO0569 lacks cysteine residues and does not contain the CxxC zinc-binding motif present in SCO4726 [ 44 ]....”

RTC6_NEUCR / Q7S4E7 Large ribosomal subunit protein bL36m from Neurospora crassa (strain ATCC 24698 / 74-OR23-1A / CBS 708.71 / DSM 1257 / FGSC 987) (see paper)
45% identity, 31% coverage

• function: Component of the mitochondrial ribosome (mitoribosome), a dedicated translation machinery responsible for the synthesis of mitochondrial genome-encoded proteins, including at least some of the essential transmembrane subunits of the mitochondrial respiratory chain. The mitoribosomes are attached to the mitochondrial inner membrane and translation products are cotranslationally integrated into the membrane.
  subunit: Component of the mitochondrial large ribosomal subunit (mt- LSU). Mature N.crassa 74S mitochondrial ribosomes consist of a small (37S) and a large (54S) subunit. The 37S small subunit contains a 16S ribosomal RNA (16S mt-rRNA) and 32 different proteins. The 54S large subunit contains a 23S rRNA (23S mt-rRNA) and 42 different proteins. bL36m has a zinc binding site.

Q71WG9 Large ribosomal subunit protein bL36 from Listeria monocytogenes serotype 4b (strain F2365)
61% identity, 100% 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
  • “...1.532 Non-allergen 146 Q71ZD0 1.746 Non-allergen 147 Q71WF4 0.935 Non-allergen 148 Q71YL9 2.126 Non-allergen 149 Q71WG9 1.537 Non-allergen 150 Q71YK0 2.221 Non-allergen 151 Q71WI2 2.143 Non-allergen 152 Q71VQ6 1.957 Non-allergen 153 Q724G8 1.5 Non-allergen 154 Q722D6 1.506 Non-allergen 155 Q71XL9 0.743 Non-allergen 156 Q720B5 0.934 Non-allergen...”

RTC6_SCHPO / O94690 Large ribosomal subunit protein bL36m; 54S ribosomal protein rtc6, mitochondrial from Schizosaccharomyces pombe (strain 972 / ATCC 24843) (Fission yeast) (see paper)
53% identity, 41% coverage

• function: Component of the mitochondrial ribosome (mitoribosome), a dedicated translation machinery responsible for the synthesis of mitochondrial genome-encoded proteins, including at least some of the essential transmembrane subunits of the mitochondrial respiratory chain. The mitoribosomes are attached to the mitochondrial inner membrane and translation products are cotranslationally integrated into the membrane. bL36m may be involved in a process influencing telomere capping.
  subunit: Component of the mitochondrial large ribosomal subunit (mt- LSU). Mature yeast 74S mitochondrial ribosomes consist of a small (37S) and a large (54S) subunit. The 37S small subunit contains a 15S ribosomal RNA (15S mt-rRNA) and at least 32 different proteins. The 54S large subunit contains a 21S rRNA (21S mt-rRNA) and at least 45 different proteins. bL36m has a zinc binding site.

BC0155 LSU ribosomal protein L36P from Bacillus cereus ATCC 14579
Q81VQ6 Large ribosomal subunit protein bL36 from Bacillus anthracis
61% identity, 100% coverage

• Variety-driven rhizosphere microbiome bestows differential salt tolerance to alfalfa for coping with salinity stress
  Fan, Frontiers in plant science 2023
  • “...(S--GC) (Catalog Number: BC0165), soil -xylosidase (S--XYS) (Catalog Number: BC4015), soil cellulase (S-CL) (Catalog Number: BC0155), soil urease (S-UE) (Catalog Number: BC0125), soil alkaline protease (S-ALPT) (Catalog Number: BC0885), soil dehydrogenase (S-DHA) (Catalog Number: BC0395), and soil alkaline phosphatase (S-ALP) (Catalog Number: BC0285) were measured according...”
• Chemical fertilizer reduction combined with bio-organic fertilizers increases cauliflower yield via regulation of soil biochemical properties and bacterial communities in Northwest China
  Xiao, Frontiers in microbiology 2022
  • “...a soil -glucosidase (S--GC) activity assay kit (BC0165) and soil cellulase (S-CL) activity assay kit (BC0155, Solarbio Biotech Co., Ltd., Beijing, China), respectively. To guarantee the validity of the experimental data, three independent tests were performed on each sample. DNA extraction and high-throughput sequencing A 16S...”
• Irrigation and Nitrogen Fertilization Alter Soil Bacterial Communities, Soil Enzyme Activities, and Nutrient Availability in Maize Crop
  Muhammad, Frontiers in microbiology 2022
  • “...phosphatase (S_ACP; BC0145), acid invertase (S_AI; BC3075), -glucosides (S_-GC; BC0165), catalase (S_CAT; BC0105), cellulose (S_CL; BC0155), and urease (S_UR; BC0125) were determined using the soil enzyme kit from Solarbio Science & Technology Co., Ltd. (Beijing, China). The methods of determination are described in detail in the...”
• Changes of bacterial and fungal communities and relationship between keystone taxon and physicochemical factors during dairy manure ectopic fermentation
  Gong, PloS one 2022
  • “...phosphatase were determined by Cellulose Assay Kit (BC0125, Solarbio, Beijing, China), Urease (UE) Assay Kit (BC0155, Solarbio, Beijing, China), Dehydrogenase (UE) Assay Kit (BC0395, Solarbio, Beijing, China) and alkaline phosphatase Assay Kit (BC0280, Solarbio, Beijing, China), respectively. All measurements were performed according to the manufacturers instructions....”
• Cysteine Proteome Reveals Response to Endogenous Oxidative Stress in Bacillus cereus
  Hamitouche, International journal of molecular sciences 2021
  • “...Transcription BC4603 Transcriptional regulator, GntR family IVC 113 NLPK 1.0 Translation, ribosomal structure, and biogenesis BC0155 50S ribosomal protein L36 (RpmJ) VRPSVKPIC 11 EK 2.2 GKVMVIC 27 ENPK Signal transduction mechanisms BC0442 Tellurium resistance protein (TerD) LSTC 79 GSIIHSGDNLTGEGAGDDETIFVELHK 1.6 LVFVVNIYDC 123 VNR Secondary metabolite biosynthesis,...”
• Methionine Sulfoxide Reductases Contribute to Anaerobic Fermentative Metabolism in Bacillus cereus
  Duport, Antioxidants (Basel, Switzerland) 2021
  • “...4.4 BC5471 RplI 50S ribosomal protein L9 1/4 QGLAAEATNSS M K 5.0 4.6 4.7 5.6 BC0155 Rpm 50S ribosomal protein L36 1/2 V M VICENPK 2.9 Uncategorized BC4182 c Gls24 Unknown 1/6 VEIAPEVIEVIAGIAAAEVEGVAA M R 2.7 3.2 3.9 3.2 a Met(O) residues that showed significant level...”
• Identification of Bacillus anthracis by using matrix-assisted laser desorption ionization-time of flight mass spectrometry and artificial neural networks
  Lasch, Applied and environmental microbiology 2009
  • “...6,491 6,643 6,679 6,835 7,082 7,165 Q6EZR7 Unassigned Q81VQ6 Q81ZB4 B0AS79 Q81Y87 Q81VA0 Q81KT1 Q81QJ2 Q6EZN2 Q81U02 Q81XK6 Unassigned Q81JG9 Unassigned Q81U86...”

RL36_DEIRA / Q9RSK0 Large ribosomal subunit protein bL36; 50S ribosomal protein L36 from Deinococcus radiodurans (strain ATCC 13939 / DSM 20539 / JCM 16871 / CCUG 27074 / LMG 4051 / NBRC 15346 / NCIMB 9279 / VKM B-1422 / R1) (see 6 papers)
3cf54 / Q9RSK0 Thiopeptide antibiotic thiostrepton bound to the large ribosomal subunit of deinococcus radiodurans (see paper)
61% identity, 100% coverage

• function: Binds the 23S rRNA
  cofactor: Zn(2+) (Binds 1 zinc ion per subunit.)
  subunit: Part of the 50S ribosomal subunit.
• Ligand: rna (3cf54)

6ywe0 / Q7S4E7 structure of the mitoribosome from Neurospora crassa in the P/E tRNA bound state (see paper)
45% identity, 83% coverage

• Ligands: rna; zinc ion (6ywe0)

3j6b0 / O14464 of the yeast mitochondrial large ribosomal subunit (see paper)
47% identity, 100% coverage

• Ligands: rna; zinc ion (3j6b0)

6z1pAG / W7XH61 6z1pAG (see paper)
50% identity, 100% coverage

• Ligands: rna; zinc ion (6z1pAG)

RTC6_YEAST / O14464 Large ribosomal subunit protein bL36m; 54S ribosomal protein RTC6, mitochondrial; Restriction of telomere capping protein 6; Translation associated element 4 from Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast) (see 6 papers)
YPL183W-A Homolog of the prokaryotic ribosomal protein L36, likely to be a mitochondrial ribosomal protein coded in the nuclear genome from Saccharomyces cerevisiae
47% identity, 41% coverage

• function: Component of the mitochondrial ribosome (mitoribosome), a dedicated translation machinery responsible for the synthesis of mitochondrial genome-encoded proteins, including at least some of the essential transmembrane subunits of the mitochondrial respiratory chain. The mitoribosomes are attached to the mitochondrial inner membrane and translation products are cotranslationally integrated into the membrane (PubMed:24675956, PubMed:25609543). bL36m may be involved in a process influencing telomere capping (PubMed:18845848, PubMed:20691087).
  subunit: Component of the mitochondrial large ribosomal subunit (mt- LSU). Mature yeast 74S mitochondrial ribosomes consist of a small (37S) and a large (54S) subunit. The 37S small subunit contains a 15S ribosomal RNA (15S mt-rRNA) and 34 different proteins. The 54S large subunit contains a 21S rRNA (21S mt-rRNA) and 46 different proteins. bL36m has a zinc binding site.
• Identification of Genes in Saccharomyces cerevisiae that Are Haploinsufficient for Overcoming Amino Acid Starvation
  Bae, G3 (Bethesda, Md.) 2017
  • “...the small (40S) ribosomal subunit; nearly identical to RPS7B M + , E, C, v YPL183W-A RTC6 Protein involved in translation; mutants have defects in biogenesis of nuclear ribosomes; sequence similar to prokaryotic ribosomal protein L36 M , C, v Protein kinase and phosphatase subunits YER133W...”
• A genomic screen revealing the importance of vesicular trafficking pathways in genome maintenance and protection against genotoxic stress in diploid Saccharomyces cerevisiae cells
  Krol, PloS one 2015
  • “..., SFB3 , SNU56 , TRL1 , TRR1 , UBP13 , YGL036W , YNR004W , YPL183W-A The zeocin-sensitive strains revealed in the genome-wide screen are divided into groups according to their ability to suppress the zeocin sensitivity phenotype on medium containing 50 mM KCl. The genes...”
• Genome-wide analysis of host factors in nodavirus RNA replication
  Hao, PloS one 2014
  • “...replication. Mitochondrial ORF Gene Molecular Function RNA1 (%WT) t1 q1 RNA3 (%WT) t3 q3 Translation YPL183W-A structural constituent of ribosome 67% 5.1 1.7% 65% 3.5 4.5% Metabolism YOL071W SDH5 oxidoreductase activity 59% 6.0 1.5% 34% 3.5 4.4% YKL148C SDH1 oxidoreductase activity 32% 13.8 0.6% 6% 41.0...”
  • “...sites of FHV RNA replication [10] , [18] . These include one mitochondrial ribosomal protein, YPL183W-A , and two subunits of the succinate dehydrogenase complex, SDH1 and SDH5 (also named EMI5 ). The remaining 5 genes encode cytoplasmic proteins, including the PRR1 and PSK2 kinases involved...”
• Identification of gold nanoparticle-resistant mutants of Saccharomyces cerevisiae suggests a role for respiratory metabolism in mediating toxicity
  Smith, Applied and environmental microbiology 2013
  • “...17, 2017 by University of California, Berkeley YPL183w-A RTC6 (1) Mitochondrial ribosomal protein of the large subunit Mitochondrial ribosomal protein of...”
  • “...3.83 105 YBR268w, YCR046c, YGR150c, YLR382c, YLR439w, YMR072w, YPL183w-A, YPR100w 6 genes (35.3) 254 genes (5.3) 0.00248 5 genes (29.4) 177 genes (3.7) 0.00437...”
• Re-annotation of protein-coding genes in the genome of saccharomyces cerevisiae based on support vector machines
  Lin, PloS one 2013
  • “...ICS3 40.90909 396 YKL037W AIM26 49.85994 357 YOR031W CRS5 42.38095 210 YPL096C-A ERI1 44.44444 207 YPL183W-A RTC6 43.97163 282 * All the 15 misclassified ORFs (with an average length of 296.6 nucleotides) are small ORFs, which are usually difficult to identify. Retrospective examination of methodology While...”
  • “...YAL064W YJL077C ICS3 98.15% YGL168W YJL028W HUR1 20072008 39 1436 100% 20082009 103 1388 YKL037W YPL183W-A AIM26 RTC6 98.06% 20092010 45 1317 100% * n new_veri denotes the number of verified genes newly added in updated snapshot of SGD database; n predicted denotes the overall predicted...”
• Chemical-genetic profile analysis of five inhibitory compounds in yeast
  Alamgir, BMC chemical biology 2010
  • “...at 30C for 1-2 days. Deletion of ypl009c confers increased sensitivity to cycloheximide; yil137c and ypl183w-a to 3-AT, ydr056c to streptomycin and neomycin, and yjr111c to streptomycin. Synthetic genetic array (SGA) analysis for TAE2 , TAE3 and TAE4 The majority of mutants with increased sensitivity to...”
  • “...studied genes were named TAE2 ( YPL009C ), TAE3 ( YIL137C ) and TAE4 ( YPL183W-A ), or translation associated elements 2-4, respectively. The largest group of genes that interacted with TAE3 and TAE4 were those involved in translation associated RNA processing, with three and seven...”
• A genomewide suppressor and enhancer analysis of cdc13-1 reveals varied cellular processes influencing telomere capping in Saccharomyces cerevisiae
  Addinall, Genetics 2008
  • “...UPF3 VPS21 VPS8 YBR147W YHR087W YNL254C YOR118W YPL183W-A YDL119C YGR201C YIL055C YIL057C YIL161W YLR404W YIL079C YER073W YPL061W YGL148W YDR101C [YMR116C...”
• Multiple pathways influence mitochondrial inheritance in budding yeast
  Frederick, Genetics 2008
  • “...RMD11 TIM13 VTS1 YDL162C YGL057C YGL226W YLR422W YPL183W-A Most genes identified as synthetic genetic interactors with gem1D encode mitochondrial proteins....”
• More

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.