PaperBLAST

PaperBLAST Hits for B158DRAFT_0779 (51 a.a., MRDKIRLVSS...)

Show query sequence

>B158DRAFT_0779
MRDKIRLVSSAGTGHFYTTDKNKKNMPGKMEIKKFDPTIRKHVIYKEAKIK

Running BLASTp...

Found 55 similar proteins in the literature:

G372_RS0107225 50S ribosomal protein L33 from Thioalkalivibrio thiocyanoxidans ARh2
90% identity, 89% 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
  • “...2.69E-11 Hypothetical protein G372_RS0106445 2.58 1.65E-24 ATP-dependent RNA helicase DeaD G372_RS0107190 2.15 1.34E-15 Guanylate kinase G372_RS0107225 1.92 9.00E-8 50S ribosomal protein L33 G372_RS0108120 1.81 5.02E-22 Hypothetical protein G372_RS0108320 2.05 1.30E-15 tRNA-Arg G372_RS0108660 2.59 1.06E-10 tRNA-Gln G372_RS0110325 1.52 1.26E-9 Membrane protein insertion efficiency factor G372_RS0110505 1.76 2.82E-17...”

VP0186 ribosomal protein L33 from Vibrio parahaemolyticus RIMD 2210633
84% identity, 91% coverage

• Insights into Vibrio parahaemolyticus CHN25 response to artificial gastric fluid stress by transcriptomic analysis
  Sun, International journal of molecular sciences 2014
  • “...2.5323 50S ribosomal protein L29 VP0255 ( rpmE ) Chn25_0246 5.0193 50S ribosomal protein L31 VP0186 ( rpmG ) Chn25_0182 7.2192 50S ribosomal protein L33 VP2030 ( rpsA ) Chn25_1918 3.9866 30S ribosomal protein S1 VP0263 ( rpsC ) Chn25_0254 2.6074 30S ribosomal protein S3 VP2740...”
• Rapid identification of Vibrio parahaemolyticus by whole-cell matrix-assisted laser desorption ionization-time of flight mass spectrometry
  Hazen, Applied and environmental microbiology 2009
  • “...protein 50S ribosomal protein L17 VP0082 VP0275 VP0186 VP2546 VP1210 VP0261 VPA1414 VP0273 VP2098 Transmembrane protein 50S ribosomal protein L30 50S...”

VC0219 ribosomal protein L33 from Vibrio cholerae O1 biovar eltor str. N16961
82% identity, 93% coverage

• Regulation of rugosity and biofilm formation in Vibrio cholerae: comparison of VpsT and VpsR regulons and epistasis analysis of vpsT, vpsR, and hapR
  Beyhan, Journal of bacteriology 2007
  • “...0.45 1.95 0.61 0.58 0.43 2.25 Other functions VC0194 VC0219 VC1825 VC1888 VC1935 VCA0074 VCA0773 VCA0864 a b 0.33 0.15 0.07 0.43 2.71 0.54 0.58 0.65 0.58...”

B7C60_RS05710 50S ribosomal protein L33 from Vibrio fujianensis
82% identity, 93% coverage

• Comparative Genomics and Transcriptomics Analyses Reveal a Unique Environmental Adaptability of Vibrio fujianensis
  Huang, Microorganisms 2020
  • “...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 Translation B7C60_RS11050 rpmA large subunit ribosomal protein L27...”

Asuc_0015 ribosomal protein L33 from Actinobacillus succinogenes 130Z
86% identity, 89% coverage

• Transcriptome analysis and anaerobic C₄ -dicarboxylate transport in Actinobacillus succinogenes
  Rhie, MicrobiologyOpen 2018
  • “...on glucose (Figure 3 , Table S4 , Table S5 ). Genes encoding ribosomal proteins (Asuc_0015, Asuc_00445, Asuc_0520, Asuc_0525, Asuc_0721, Asuc_0774, Asuc_14934, and Asuc_2117) and their accessory proteins were among those classified into this cluster. In addition, members of the betaglucoside operon (Asuc_09725) and 11 genes...”

HI0950 ribosomal protein L33 (rpL33) from Haemophilus influenzae Rd KW20
86% identity, 89% coverage

• Initial proteome analysis of model microorganism Haemophilus influenzae strain Rd KW20
  Kolker, Journal of bacteriology 2003
  • “...HI0782 HI0779 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...”

APL_1972 50S ribosomal protein L33 from Actinobacillus pleuropneumoniae L20
86% identity, 89% coverage

• Host-pathogen interactions of Actinobacillus pleuropneumoniae with porcine lung and tracheal epithelial cells
  Auger, Infection and immunity 2009
  • “...APL_0223 APL_1773 APL_1775 APL_0399 APL_1401 APL_1972 APL_0040 APL_1228 APL_0678 APL_1781 APL_1383 APL_0641 APL_1476 APL_1789 HOST-PATHOGEN INTERACTIONS...”

7m4v0 / A0A7U4DFF9 A. Baumannii ribosome-eravacycline complex: 50s (see paper)
HMPREF0010_01791 50S ribosomal protein L33 from Acinetobacter baumannii ATCC 19606 = CIP 70.34 = JCM 6841
A1S_0447 50S ribosomal protein L33 from Acinetobacter baumannii ATCC 17978
AB57_0530 ribosomal protein L33 from Acinetobacter baumannii AB0057
ACIAD0501 50S ribosomal protein L33 from Acinetobacter sp. ADP1
84% identity, 100% coverage

• Ligand: rna (7m4v0)
• Delineating the Plausible Molecular Vaccine Candidates and Drug Targets of Multidrug-Resistant Acinetobacter baumannii
  Mujawar, Frontiers in cellular and infection microbiology 2019
  • “...A1S_0147 HMPREF0010_02008 A1S_0217 HMPREF0010_01991 A1S_0236 HMPREF0010_01903 A1S_0334 HMPREF0010_01875 A1S_0364 HMPREF0010_01854 A1S_0388 HMPREF0010_01851 A1S_0391 HMPREF0010_01810 A1S_0428 HMPREF0010_01791 A1S_0447 HMPREF0010_01758 A1S_0469 HMPREF0010_01757 A1S_0470 HMPREF0010_01723 A1S_0506 HMPREF0010_01691 A1S_0561 HMPREF0010_01682 A1S_0571 KFC HMPREF0010_02522 HMPREF0010_02769 HMPREF0010_03233 HMPREF0010_00091 A1S_2232 HMPREF0010_03207 HMPREF0010_01641 HMPREF0010_03022 HMPREF0010_02437 A1S_3280 HMPREF0010_01350 HMPREF0010_01047 Table 6 The human counterparts of...”
• Novel Genes Required for Surface-Associated Motility in Acinetobacter baumannii
  Blaschke, Current microbiology 2021
  • “...N.s. N.s. A1S_1624 Ap4A hydrolase ++ Y N.s. N.s. N.s. S*** N.s. RNA modification/ regulation A1S_0447 rpmG 50S ribosomal protein L33 +++ Y N.s. N.s. N.s. S* S** A1S_0778 metG Methionyl-tRNA synthetase +++ Y **** **** N.s. N.s. S*** A1S_2182 gidA Glucose-inhibited division protein A, FAD-binding...”
  • “...0.10 0.03 0.9 2.0 A1S_0414 106.6 32.0 0.23 0.25 1.6 2.0 A1S_1624 32 0.125 2.1 A1S_0447 rpmG 29.3 0.16 1.0 A1S_0778 metG 32 0.23 0.46 A1S_0530 24 0.19 2.0 A1S_3366 gshA 85.3 26.6 0.29 0.23 1.6 2.0 A1S_1970 64 32.0 0.16 0.25 2.5 1.8 A1S_2840 ompA...”
• Delineating the Plausible Molecular Vaccine Candidates and Drug Targets of Multidrug-Resistant Acinetobacter baumannii
  Mujawar, Frontiers in cellular and infection microbiology 2019
  • “...HMPREF0010_02008 A1S_0217 HMPREF0010_01991 A1S_0236 HMPREF0010_01903 A1S_0334 HMPREF0010_01875 A1S_0364 HMPREF0010_01854 A1S_0388 HMPREF0010_01851 A1S_0391 HMPREF0010_01810 A1S_0428 HMPREF0010_01791 A1S_0447 HMPREF0010_01758 A1S_0469 HMPREF0010_01757 A1S_0470 HMPREF0010_01723 A1S_0506 HMPREF0010_01691 A1S_0561 HMPREF0010_01682 A1S_0571 KFC HMPREF0010_02522 HMPREF0010_02769 HMPREF0010_03233 HMPREF0010_00091 A1S_2232 HMPREF0010_03207 HMPREF0010_01641 HMPREF0010_03022 HMPREF0010_02437 A1S_3280 HMPREF0010_01350 HMPREF0010_01047 Table 6 The human counterparts of the...”
• The lytic transglycosylase MltB connects membrane homeostasis and in vivo fitness of Acinetobacter baumannii
  Crépin, Molecular microbiology 2018
  • “...0.0031 AB57_3680 acetyltransferase 9.37 0.0062 AB57_2749 lytic transglycosylase 9.36 0.0000 AB57_2865 NUDIX hydrolase 9.24 0.0022 AB57_0530 50S ribosomal protein L33 9.24 0.0001 AB57_0531 50S ribosomal protein L28 9.24 0.0001 AB57_0459 hypothetical protein 9.21 0.0052 AB57_0336 glutamylQ tRNA(Asp) ligase 9.17 0.0000 AB57_3836 phosphoserine phosphatase 9.16 0.0035 AB57_2526...”
• iTRAQ-Based Comparative Proteomic Analysis of Acinetobacter baylyi ADP1 Under DNA Damage in Relation to Different Carbon Sources
  Jiang, Frontiers in microbiology 2019
  • “...DNA-binding transcriptional regulator HcaR hcaR ACIAD0448 0.38 0.49 0.22 0.3 50S ribosomal protein L33 rpmG ACIAD0501 0.45 0.77 0.33 0.4 50S ribosomal protein L28 rpmB ACIAD0502 0.52 0.65 0.39 0.53 30S ribosomal protein S12 rpsL ACIAD0881 0.37 0.49 0.3 0.51 BetI family transcriptional regulator betI ACIAD1010...”

Pput_5191 50S ribosomal protein L33 from Pseudomonas putida F1
PP_5281 ribosomal protein L33 from Pseudomonas putida KT2440
78% identity, 100% coverage

• iTRAQ-based quantitative proteomic analysis of the global response to 17β-estradiol in estrogen-degradation strain Pseudomonas putida SJTE-1
  Xu, Scientific reports 2017
  • “...0.004 gi|148550410 DNA-directed RNA polymerase subunit omega Pput_5210 1.63 0.041 gi|148550391 50S ribosomal protein L33 Pput_5191 3.19 0.006 Other proteins gi|148546021 Phosphoribosyltransferase Pput_0775 1.73 0.000 gi|148549587 cell division protein FtsZ Pput_4382 0.65 0.002 gi|148549586 UDP-3-O-[3hydroxymyristoyl] N-acetylglucosamine deacetylase Pput_4381 0.59 0.001 gi|148549970 Protease FtsH subunit HflK Pput_4768...”
• H-NS Family Proteins Drastically Change Their Targets in Response to the Horizontal Transfer of the Catabolic Plasmid pCAR1
  Nakamura, Frontiers in microbiology 2020
  • “...30S ribosomal protein S6 PP_5027 dtD D -Tyrosyl-tRNA(Tyr) deacylase PP_5087 rpmE 50S ribosomal protein L31 PP_5281 rpmG 50S ribosomal protein L33 PP_5282 rpmB 50S ribosomal protein L28 Next, we sorted the differentially transcribed genes in KT2440 turA (pCAR1) and KT2440 turB (pCAR1) in the stationary phase...”

PD0489 50S ribosomal protein L33 from Xylella fastidiosa Temecula1
80% identity, 93% coverage

• Characterization of regulatory pathways in Xylella fastidiosa: genes and phenotypes controlled by algU
  Shi, Applied and environmental microbiology 2007
  • “...PD0444 PD0445 PD0447 PD0450 PD0451 PD0452 PD0454 PD0455 PD0458 PD0488 PD0489 PD0749 50S 50S 50S 50S 50S 30S 30S 50S 30S 50S 30S 50S 50S 50S 0.449 0.499 0.426...”

Q5GU11 Large ribosomal subunit protein bL33 from Xanthomonas oryzae pv. oryzae (strain KACC10331 / KXO85)
78% identity, 91% coverage

• Antibacterial Activities and Underlying Mechanisms of the Compound SYAUP-491 against Xanthomonas oryzae pv. oryzae
  Li, Molecules (Basel, Switzerland) 2024
  • “...L29 xoo:XOO3575 0.446445 0.001933 RL34_XANOR Q05HP6 rpmH 50S ribosomal protein L34 xoo:XOO4957 0.121112 0.003118 RL33_XANOR Q5GU11 rpmG 50S ribosomal protein L33 xoo:XOO4558 0.101754 0.000052...”

7unr5 / Q9HTN9 7unr5
Q9HTN9 Large ribosomal subunit protein bL33 from Pseudomonas aeruginosa (strain ATCC 15692 / DSM 22644 / CIP 104116 / JCM 14847 / LMG 12228 / 1C / PRS 101 / PAO1)
PA14_70180 50S ribosomal protein L33 from Pseudomonas aeruginosa UCBPP-PA14
PA5315 50S ribosomal protein L33 from Pseudomonas aeruginosa PAO1
IHMA87_05840 50S ribosomal protein L33 from Pseudomonas aeruginosa
78% identity, 100% coverage

• Ligand: rna (7unr5)
• Proteomic Analysis of Vesicle-Producing Pseudomonas aeruginosa PAO1 Exposed to X-Ray Irradiation
  Zhang, Frontiers in microbiology 2020
  • “...Probable binding protein component of ABC iron transporter Q9HTP9 PA5305 1.581 0.412 3.83 Uncharacterized protein Q9HTN9 PA5315 RpmG 1.86 0.28 6.643 50S ribosomal protein Q9HTM5 PA5330 1.828 0.488 3.75 Uncharacterized protein Q9HTL0 PA5348 HupA 0.869 0.381 2.281 DNA-binding protein HU-alpha Q9HTF0 PA5414 1.308 0.616 2.12 Uncharacterized...”
• Top-Down LESA Mass Spectrometry Protein Analysis of Gram-Positive and Gram-Negative Bacteria
  Kocurek, Journal of the American Society for Mass Spectrometry 2017
  • “...C Storage: 18 days, 4 C fMet Pseudomonas aeruginosa PS1054 672.2674 +9 6041.34 -1.8 L33 Q9HTN9 31 Incubation and storage: 4 days, 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...”
• Loss of the Two-Component System TctD-TctE in Pseudomonas aeruginosa Affects Biofilm Formation and Aminoglycoside Susceptibility in Response to Citric Acid
  Taylor, mSphere 2019
  • “...Regulatory protein TypA 2.93 PA14_52340 3.04 PA14_27370 3.52 PA14_15970 rpsP 30S ribosomal protein S16 3.55 PA14_70180 rpmG 50S ribosomal protein L33 3.59 PA14_15990 trmD tRNA (guanine-N1)-methyltransferase 3.60 PA14_39060 4.14 Biofilm PA14_72260 5.54 PA14_02520 5.26 PA14_42860 3.51 PA14_46900 3.41 PA14_56540 2.94 PA14_55750 2.92 PA14_22350 2.52 PA14_56690 2.47...”
• Virtual Screening and Meta-Analysis Approach Identifies Factors for Inversion Stimulation (Fis) and Other Genes Responsible for Biofilm Production in <i>Pseudomonas aeruginosa</i>: A Corneal Pathogen
  Emeka, Current issues in molecular biology 2024
  • “...P protein component 1.53 8.64 10 10 PA5555 atpG ATP synthase gamma chain 1.48 0.0023 PA5315 rpmG 50S ribosomal protein L33 1.48 8.82 10 12 PA4932 rplI 50S ribosomal protein L9 1.48 1.22 10 6 PA4744 infB translation initiation factor IF-2 1.45 0.0020 PA0904 lysC aspartate...”
• Distinct transcriptome and traits of freshly dispersed <i>Pseudomonas aeruginosa</i> cells
  Kalia, mSphere 2024
  • “...1.759096 PA5098 hutH-histidine ammonia-lyase Upregulated 1.021263 Upregulated 0.482614 PA5119 glnA-glutamine synthetase Upregulated 0.474793 Upregulated 0.541001 PA5315 50S ribosomal protein L33 Upregulated 0.84785 Upregulated 0.761561 PA5366 ATP binding component of ABC phosphate transporter Upregulated 1.401961 Upregulated 0.735852 PA5427 Alcohol dehydrogenase 0.79947 Upregulated 0.06287 PA5490 cc4-cytochrome c4 precursor...”
• Genome-wide screen in human plasma identifies multifaceted complement evasion of Pseudomonas aeruginosa
  Janet-Maitre, PLoS pathogens 2023
  • “...5.21E-16 IHMA87_00896 PA4032 -/ probable response regulator 9.89 3.67E-24 IHMA87_03447 PA1758 pabB 9.79 2.55E-22 IHMA87_05840 PA5315 rpmG 9.71 2.60E-07 IHMA87_03022 PA2122 -/lipid biosynthetic process 9.65 1.27E-13 IHMA87_01755 NA - 9.51 7.37E-23 IHMA87_04617 PA4315 mvaT 9.41 1.21E-23 IHMA87_02603 NA - 9.34 4.46E-17 IHMA87_02570 NA - 9.28 3.29E-13...”
• The Small RNAs PA2952.1 and PrrH as Regulators of Virulence, Motility, and Iron Metabolism in Pseudomonas aeruginosa
  Coleman, Applied and environmental microbiology 2021 (secret)
• Full Transcriptomic Response of Pseudomonas aeruginosa to an Inulin-Derived Fructooligosaccharide
  Rubio-Gómez, Frontiers in microbiology 2020
  • “...Uncharacterized protein 0.7 0.002 0.7 0.003 PA5301 pauR Polyamine catabolic process 0.7 0.002 0.6 0.002 PA5315 rpmG 50S ribosomal protein L33 0.6 0.002 0.6 0.001 PA5332 crc Catabolite repression control protein 1.1 0.000 0.8 0.004 PA5348 nd Probable DNA-binding protein 0.6 0.010 0.7 0.005 PA5367 pstA...”
  • “...0.000 PA5288 glnK Nitrogen regulatory protein 0.6 0.003 PA5301 pauR Polyamine catabolic process 0.9 0.000 PA5315 rpmG 50S ribosomal protein L33 0.7 0.000 PA5332 crc Catabolite repression control protein 0.7 0.000 PA5348 Probable DNA-binding protein 0.7 0.001 PA5367 pstA Phosphate ABC transporter 0.7 0.001 PA5369 pstS...”
• Proteomic Analysis of Vesicle-Producing Pseudomonas aeruginosa PAO1 Exposed to X-Ray Irradiation
  Zhang, Frontiers in microbiology 2020
  • “...binding protein component of ABC iron transporter Q9HTP9 PA5305 1.581 0.412 3.83 Uncharacterized protein Q9HTN9 PA5315 RpmG 1.86 0.28 6.643 50S ribosomal protein Q9HTM5 PA5330 1.828 0.488 3.75 Uncharacterized protein Q9HTL0 PA5348 HupA 0.869 0.381 2.281 DNA-binding protein HU-alpha Q9HTF0 PA5414 1.308 0.616 2.12 Uncharacterized protein...”
• σ Factor and Anti-σ Factor That Control Swarming Motility and Biofilm Formation in Pseudomonas aeruginosa
  McGuffie, Journal of bacteriology 2015
  • “...PA2896 PA3179 PA3569 PA3570 PA3876 PA3923 PA4495 PA5172 PA5315 PA5435 PA5445 PAO1 sbrR pPSV38 vs. PAO1 pPSV38 ical triplicate or quadruplicate on three separate...”
• Microarray analysis of Pseudomonas aeruginosa reveals induction of pyocin genes in response to hydrogen peroxide
  Chang, BMC genomics 2005
  • “...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 E. coli sulA [ 20 ], showed increased transcript...”
  • “...( 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 618.6 109.2 0.008 5.7 Cellular protective mechanism-related PA4236 ( katA ) 543.8 275.1 0.008 2.0 PA4613 (...”
• Genome-wide screen in human plasma identifies multifaceted complement evasion of Pseudomonas aeruginosa
  Janet-Maitre, PLoS pathogens 2023
  • “...9.95 5.21E-16 IHMA87_00896 PA4032 -/ probable response regulator 9.89 3.67E-24 IHMA87_03447 PA1758 pabB 9.79 2.55E-22 IHMA87_05840 PA5315 rpmG 9.71 2.60E-07 IHMA87_03022 PA2122 -/lipid biosynthetic process 9.65 1.27E-13 IHMA87_01755 NA - 9.51 7.37E-23 IHMA87_04617 PA4315 mvaT 9.41 1.21E-23 IHMA87_02603 NA - 9.34 4.46E-17 IHMA87_02570 NA - 9.28...”

PMCN03_0012 50S ribosomal protein L33 from Pasteurella multocida subsp. multocida str. HB03
78% identity, 89% 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
  • “...2 Forty putative secreted proteins of P. multocida HB03 genome. Numbers Putative proteins Description 1 PMCN03_0012 50S ribosomal protein L33, rpl33 2 PMCN03_0067 DNA-binding protein Fis, Fis 3 PMCN03_0121 Galactose-1-phohate uridylyltransferase, galT 4 PMCN03_0141 Polysaccharide export protein Wza 5 PMCN03_0287 Hypothetical protein 6 PMCN03_0519 30S ribosomal...”

SG2207 50S ribosomal protein L33 from Sodalis glossinidius str. 'morsitans'
76% identity, 93% coverage

• Quorum sensing primes the oxidative stress response in the insect endosymbiont, Sodalis glossinidius
  Pontes, PloS one 2008
  • “...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 (SG1908) and a putative ribosome modulation factor (SG1025) also displayed reduced...”

5aka1 / P0A7N9 Em structure of ribosome-srp-ftsy complex in closed state (see paper)
75% identity, 94% coverage

• Ligand: rna (5aka1)

A1JHR4 Large ribosomal subunit protein bL33 from Yersinia enterocolitica serotype O:8 / biotype 1B (strain NCTC 13174 / 8081)
75% identity, 93% coverage

• Deconvolution and database search of complex tandem mass spectra of intact proteins: a combinatorial approach
  Liu, Molecular & cellular proteomics : MCP 2010
  • “...11 12 11 12 13 13 9 10 A1JS21 A1JS24 A1JIJ4 A1JK22 A1JNM8 A1JS33 A1JRC9 A1JHR4 109 85 81 241 216 85 98 97 53 42 37 51 66 38 63 36 40 29 34 36 49 26 49 25 161,...”

RpmG / b3636 50S ribosomal subunit protein L33 from Escherichia coli K-12 substr. MG1655 (see 56 papers)
rpmG / P0A7N9 50S ribosomal subunit protein L33 from Escherichia coli (strain K12) (see 54 papers)
RL33_ECOLI / P0A7N9 Large ribosomal subunit protein bL33; 50S ribosomal protein L33 from Escherichia coli (strain K12) (see 10 papers)
Z5060 50S ribosomal subunit protein L33 from Escherichia coli O157:H7 EDL933
NP_418093 50S ribosomal subunit protein L33 from Escherichia coli str. K-12 substr. MG1655
P0A7P2 Large ribosomal subunit protein bL33 from Salmonella typhimurium (strain LT2 / SGSC1412 / ATCC 700720)
EAMY_0078 50S ribosomal protein L33 from Erwinia amylovora CFBP1430
b3636 50S ribosomal protein L33 from Escherichia coli str. K-12 substr. MG1655
SEN3549 50S ribosomal subunit protein L33 from Salmonella enterica subsp. enterica serovar Enteritidis str. P125109
ECs4511 50S ribosomal subunit protein L33 from Escherichia coli O157:H7 str. Sakai
SENTW_3828 50S ribosomal protein L33 from Salmonella enterica subsp. enterica serovar Weltevreden str.
75% identity, 93% coverage

• subunit: Part of the 50S ribosomal subunit (PubMed:10094780, PubMed:12809609, PubMed:16272117, PubMed:24844575, PubMed:25310980, PubMed:27906160, PubMed:27906161, PubMed:27934701, PubMed:786732). Cross-links to the P and E site tRNAs (PubMed:8524654).
• Transcriptional responses of Escherichia coli K-12 and O157:H7 associated with lettuce leaves
  Fink, Applied and environmental microbiology 2012
  • “...Z4675 Z5556 Z4589 Z4680 Z4674 Z4689 Z4679 Z3444 Z5061 Z5060 Z5194 Z0180 Z4666 Z4673 Z5809 Z4676 Z4692 Z4667 Z4700 Z4668 Z4677 Z4526 Z3903 Z5811 Z0027 Z4418...”
• Identification of Escherichia coli ygaQ and rpmG as novel mitomycin C resistance factors implicated in DNA repair.
  Bolt, Bioscience reports 2015
  • GeneRIF: expression of ygaQ and rpmG promotes mitomycin C resistance (MMC(R)).
• Primary structure of protein L33 from the large subunit of the Escherichia coli ribosome.
  Wittmann-Liebold, FEBS letters 1976 (PubMed)
  • GeneRIF: N-terminus verified by Edman degradation on mature peptide
• Comparing Top-Down Proteoform Identification: Deconvolution, PrSM Overlap, and PTM Detection
  Tabb, Journal of proteome research 2023
  • “...yield. The proteoform that represented the most PrSMs gained in the UniProtKB XML search was P0A7N9 (50S ribosomal protein L33), with the N-terminal Met clipped and the Ala at position two methylated (rather than acetylated). By itself, this proteoform accounted for 106 PrSMs, making it the...”
• FLASHIda enables intelligent data acquisition for top-down proteomics to boost proteoform identification counts
  Jeong, Nature communications 2022
  • “...same protein were also often two orders of magnitude apart (e.g., UniProtKB: P0A7N1, P0A7K2, and P0A7N9). In addition to ribosomal proteins, various proteins from distinct components including intracellular organelles, cytosol, and cytoplasm were identified in FI90s datasets. Not surprisingly, membrane proteins were rarely reported, indicating that...”
• Capturing Membrane Protein Ribosome Nascent Chain Complexes in a Native-like Environment for Co-translational Studies
  Pellowe, Biochemistry 2020
  • “...RL25, P68919; RL27, P0A7M0; RL28, P0A7M2; RL29, P0A7M6; RL30, P0AG51; RL31, P0A7M9; RL32, C4ZS29; RL33, P0A7N9; RL34, P0A7P6; RL35, P0A7Q2; RL36, P0A7Q7. Author Contributions G.A.P., E.R., and P.J.B. designed the research. G.A.P., H.E.F., K.L., T.M.G., and E.R. performed all experiments and analyses, except for SecYEG preparation,...”
• Characterization of Proteoforms with Unknown Post-translational Modifications Using the MIScore
  Kou, Journal of proteome research 2016
  • “...ID: P0A7K2) and the N-terminal methylation site A2 in the protein RL33 ECOLI (UniProt ID: P0A7N9) were supported by the annotations. One main reason for the lack of support by the annotations is that the annotation of the EC proteome is incomplete in the Swiss-Prot database....”
• Optimization of parameters for coverage of low molecular weight proteins
  Müller, Analytical and bioanalytical chemistry 2010
  • “...These proteins include highly abundant ribosomal proteins like the 50S ribosomal protein L33 (SwissProt entry: P0A7N9, 186,000,000 copies/cell) as well as rare proteins with less than 200 copies per cell such as Acyl-CoA thioesterase I (SwissProt entry: P0ADA1, 186 copies/cell). Furthermore, we identified about 100 proteins...”
• N-dodecanoyl-homoserine lactone influences the levels of thiol and proteins related to oxidation-reduction process in Salmonella
  de, PloS one 2018
  • “...Translation ND ND ND ND ND ND 10.159 1.074 ND ND 50S ribosomal protein L33 P0A7P2 rpmG Translation ND ND 8.313 2.037 ND ND 7.849 1.076 ND ND 50S ribosomal protein L34 P0A7P8 rpmH Translation -7.903 2.324 ND ND ND ND 9.446 1.053 ND ND 30S...”
• The stringent response regulator (p) ppGpp mediates virulence gene expression and survival in Erwinia amylovora
  Yang, BMC genomics 2020
  • “..., ribosomal protein L4 1.15 10.38 rpm EAMY_0136 rpmE , ribosomal protein L31 2.64 9.97 EAMY_0078 rpmG , ribosomal protein L33 2.43 10.07 EAMY_3368 rpmD , ribosomal protein L30 1.8 10.52 EAMY_0077 rpmB , ribosomal protein L28 1.76 10.47 EAMY_0333 rpmA , ribosomal protein L27 1.64...”
• In vitro transcription profiling of the σS subunit of bacterial RNA polymerase: re-definition of the σS regulon and identification of σS-specific promoter sequence elements
  Maciag, Nucleic acids research 2011
  • “...Ribosomal maturation protein b3170 2.01 rpsF Ribosomal protein S6 b4200 2.04 rpmG Ribosomal protein L33 b3636 2.10 relA ppGpp alarmone biosynthetic enzyme b2784 2.35 rplU Ribosomal protein L21, in rplU-rpmA operon b3186 2.50 rpmA Ribosomal protein L27, in rplU-rpmA operon b3185 2.58 rpsU Ribosomal protein S21...”
• Depletion of the non-coding regulatory 6S RNA in E. coli causes a surprising reduction in the expression of the translation machinery
  Neusser, BMC genomics 2010
  • “...protein L19 b3934 cytR 0.56 DNA-binding transcriptional dual regulator b2608 rimM 0.56 16S rRNA-processing protein b3636 rpmG 0.55 50S ribosomal protein L33 b0162 cdaR 0.54 DNA-binding transcriptional activator b4201 priB 0.54 primosomal replication protein N (S6 operon) b3988 rpoC 0.54 DNA-directed RNA polymerase subunit beta' (L10...”
• Analysis of promoter targets for Escherichia coli transcription elongation factor GreA in vivo and in vitro
  Stepanova, Journal of bacteriology 2007
  • “...b3618 1.6 Involved in lipopolysaccharide biosynthesis rpmG rpmB b3636 b3637 2.4 2.6 50S ribosomal subunit protein L33 50S ribosomal subunit protein L28 rpmH...”
• YdgG (TqsA) controls biofilm formation in Escherichia coli K-12 through autoinducer 2 transport
  Herzberg, Journal of bacteriology 2006
  • “...b3317 b3318 b3321 b3316 b3319 b3315 b3314 b3637 b0169 b4200 b3186 b4202 b3636 b3983 b3313 b3312 8.6 8 7.5 7.5 7.5 6.1 6.1 6.1 5.3 5.3 5.3 4.9 4.9 4.6 4.3 4 4...”
• 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
  • “...yjjS yjjT 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...”
• Global transcriptomic analysis of ethanol tolerance response in Salmonella Enteritidis
  He, Current research in food science 2022
  • “...L24 SEN3136 rpmA 3.44 50S ribosomal protein L27 SEN4157 rpsF 3.30 30S ribosomal protein S6 SEN3549 rpmG 2.16 50S ribosomal protein L33 SEN3246 rpsM 3.41 30S ribosomal protein S13 SEN3259 rpsQ 4.77 30S ribosomal protein S17 SEN0450 rpmE2 5.27 50S ribosomal protein L31 SEN3137 rplU 2.89...”
• Global transcriptional response of Escherichia coli O157:H7 to growth transitions in glucose minimal medium
  Bergholz, BMC microbiology 2007
  • “...yibH 3.78 2 ECs4168 rpsE -3.75 1 ECs4475 mtlA 2.84 2 ECs4169 rplR -3.75 1 ECs4511 rpmG -3.21 1 ECs4170 rplF -3.62 1 ECs4514 dfp -2.28 1 ECs4171 rpsH -4.00 1 ECs4554 espB -2.41 1 ECs4172 rpsN -3.13 1 ECs4555 espD -2.60 1 ECs4173 rplE -4.26...”
• Transcriptional profile of Salmonella enterica subsp. enterica serovar Weltevreden during alfalfa sprout colonization
  Brankatschk, Microbial biotechnology 2014
  • “...rpmD SENTW_3549 3.82 50S ribosomal protein L30 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...”

A6TFM7 Large ribosomal subunit protein bL33 from Klebsiella pneumoniae subsp. pneumoniae (strain ATCC 700721 / MGH 78578)
B5XTG7 Large ribosomal subunit protein bL33 from Klebsiella pneumoniae (strain 342)
75% identity, 93% coverage

• Comparative Proteomics of Outer Membrane Vesicles from Polymyxin-Susceptible and Extremely Drug-Resistant Klebsiella pneumoniae
  Hussein, mSphere 2023
  • “...protein L19 Cytoplasmic A6TEY0 rpsL 30S ribosomal protein S12 Cytoplasmic A6TF49 glgC Glucose-1-phosphate adenylyltransferase Cytoplasmic A6TFM7 rpmG 50S ribosomal protein L33 Cytoplasmic A6TFN2 slmA Nucleoid occlusion factor SlmA Cytoplasmic A6TBW5 nuoK NADH-quinone oxidoreductase subunit K Cytoplasmic membrane A6TGH3 wzz ECA polysaccharide chain length modulation protein Cytoplasmic...”
• Disruption of KPC-producing Klebsiella pneumoniae membrane via induction of oxidative stress by cinnamon bark (Cinnamomum verum J. Presl) essential oil
  Yang, PloS one 2019
  • “...7.07 2 Beta-galactosidase 2 lacZ2 A6TI29 Carbohydrate metabolism 4.65 3 50S ribosomal protein L33 rpmG B5XTG7 Protein biosynthesis 3.97 4 Sucrose porin scrY P27218 Transport 3.05 5 ATP-dependent protease ATPase subunit HslU hslU B5XZ37 Stress response 2.68 6 Uridine phosphorylase udp P52671 Pyrimidine biosynthesis 2.57 7...”

bglu_1g28690 50S ribosomal protein L33 from Burkholderia glumae BGR1
78% identity, 91% coverage

• RNAseq-based Transcriptome Analysis of Burkholderia glumae Quorum Sensing
  Kim, The plant pathology journal 2013
  • “...0.9 1.3 1.2 bglu_1g25990 rpsO 0.6 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...”

8rd8bk / A0A0M4SWV1 8rd8bk (see paper)
76% identity, 96% coverage

• Ligand: rna (8rd8bk)

WQ49_RS26625 50S ribosomal protein L33 from Burkholderia cenocepacia
78% identity, 91% coverage

• Identification of putative essential protein domains from high-density transposon insertion sequencing
  Rahman, Scientific reports 2022
  • “...Domain (CxxC_CXXC_SSSS) WQ49_RS25680 BCAL0909 16S rRNA maturation RNase YbeY Endoribonuclease activity 68 0 Domain (UPF0054) WQ49_RS26625 BCAL2715 RpmG Structural constituent of ribosome 0 31 Domain (Ribosomal_L33) WQ49_RS27920 BCAL2334 NADH-quinone oxidoreductase subunit K NADH dehydrogenase 0 21 Domain (Oxidored_q2) WQ49_RS28635 BCAL2199 FeS cluster assembly transcriptional regulator IscR...”

BTH_I0779 ribosomal protein L33 from Burkholderia thailandensis E264
BPSL0915 50S ribosomal protein L33 from Burkholderia pseudomallei K96243
78% identity, 91% coverage

• Gene and protein expression in response to different growth temperatures and oxygen availability in Burkholderia thailandensis
  Peano, PloS one 2014
  • “...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 ( rpsO ) S15P/S13E 2.30 1.2 All BTH_I1140 (...”
• 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
  • “...BPSL3261, many 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...”
  • “...BPSS0394 (antitoxin BrnA) and BPSS0390 (toxin HicA), and different genes that encodes for ribosomal-related proteins (BPSL0915, BPSL1461, BPSL1942, BPSL1943, BPSL2444, BPSL3194, BPSL3196, BPSL3197, BPSL3209, and BPSL3217). It is important to highlight a putative new TA system, encoded by BPSS1821-BPSS1820, that exhibits identity homology with the MbcTA...”
• Genetic and transcriptional analysis of the siderophore malleobactin biosynthesis and transport genes in the human pathogen Burkholderia pseudomallei K96243
  Alice, Journal of bacteriology 2006
  • “...those involved in protein biosynthesis (e.g., BPSS1716, BPSL0915, BPSL1943, and BPSL1962) were down-regulated. ORFs BPSS1162 and BPSS1163 showed the widest...”

BCAL2715 50S ribosomal protein L33 from Burkholderia cenocepacia J2315
76% identity, 91% coverage

• Identification of putative essential protein domains from high-density transposon insertion sequencing
  Rahman, Scientific reports 2022
  • “...(CxxC_CXXC_SSSS) WQ49_RS25680 BCAL0909 16S rRNA maturation RNase YbeY Endoribonuclease activity 68 0 Domain (UPF0054) WQ49_RS26625 BCAL2715 RpmG Structural constituent of ribosome 0 31 Domain (Ribosomal_L33) WQ49_RS27920 BCAL2334 NADH-quinone oxidoreductase subunit K NADH dehydrogenase 0 21 Domain (Oxidored_q2) WQ49_RS28635 BCAL2199 FeS cluster assembly transcriptional regulator IscR DNA-binding...”

PVU19_RS06060, SPO2965 50S ribosomal protein L33 from Roseovarius tolerans
65% identity, 87% coverage

• Chemical quantification of N-acyl alanine methyl ester (NAME) production and impact on temporal gene expression patterns in Roseovarius tolerans EL-164
  Leinberger, BMC microbiology 2024
  • “...Genes in cluster 1 mostly corresponded to primary metabolism and encode components of ribosomal subunits (PVU19_RS06060, PVU19_RS07965, PVU19_RS08950, PVU19_RS18125), ubiquinone biosynthesis (PVU19_RS01000, PVU19_RS01250), diverse transporters (e.g., PVU19_RS02070, PVU19_RS02405, PVU19_RS02835, PVU19_RS03345, PVU19_RS05975, PVU19_RS06130) and the general regulator sigma factor 70 (PVU19_RS11495) (Supplement F3 ). As expected, these...”
• Experimental Identification of Small Non-Coding RNAs in the Model Marine Bacterium Ruegeria pomeroyi DSS-3
  Rivers, Frontiers in microbiology 2016
  • “...1.35 0.485 cis70 224 SPO2940 Serine hydroxymethyltransferase Amino acid metabolism Antisense 1.40 NA cis71 186 SPO2965 Ribosomal protein L33 Translation Antisense 2.50 0.091 cis72 455 SPO2994 Peptide/nickel/opine transporter, periplasmic Transport Antisense 1.62 0.479 cis73 401 SPO2022 Valyl-tRNA synthetase Translation Antisense 1.22 0.805 cis74 173 SPO3036 Metallo-B-lactamase...”

RL33_DEIRA / Q9RSS4 Large ribosomal subunit protein bL33; 50S ribosomal protein L33 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)
50% identity, 84% coverage

• function: Binds the 23S rRNA and the E site tRNA
  subunit: Part of the 50S ribosomal subunit. Contacts protein L35.

4io91 / Q9RSS4 Crystal structure of compound 4d bound to large ribosomal subunit (50s) from deinococcus radiodurans (see paper)
51% identity, 85% coverage

• Ligand: rna (4io91)

RL33_RHOPA / Q6N554 Large ribosomal subunit protein bL33; 50S ribosomal protein L33; RRP-L33 from Rhodopseudomonas palustris (strain ATCC BAA-98 / CGA009) (see paper)
RPA3129 50S ribosomal protein L33 from Rhodopseudomonas palustris CGA009
60% identity, 87% coverage

• ATP Is a Major Determinant of Phototrophic Bacterial Longevity in Growth Arrest
  Yin, mBio 2023
  • “...to right, 50S ribosome: RPA0038, RPA0039, RPA0158, RPA0159, RPA0241, RPA0493, RPA0526, RPA0634, RPA0918, RPA2767, RPA3080, RPA3129, RPA3225, RPA3231, RPA3232, RPA3234, RPA3235, RPA3238, RPA3239, RPA3240, RPA3242, RPA3243, RPA3245, RPA3247-RPA3250, RPA3269, RPA3270, RPA3272, RPA3273, RPA4197, RPA4356; 30S ribosome: RPA0064, RPA0244, RPA0433, RPA1589, RPA2768, RPA2922, RPA3077, RPA3078, RPA3227, RPA3228,...”

8a22AA 8a22AA (see paper)
46% identity, 98% coverage

• Ligand: rna (8a22AA)

7pktz / A8J9C3 7pktz (see paper)
49% identity, 92% coverage

• Ligand: rna (7pktz)

SMc01369 PROBABLE 50S RIBOSOMAL PROTEIN L33 from Sinorhizobium meliloti 1021
56% identity, 87% coverage

• Antimicrobial nodule-specific cysteine-rich peptides induce membrane depolarization-associated changes in the transcriptome of Sinorhizobium meliloti
  Tiricz, Applied and environmental microbiology 2013
  • “...SMc01313 SMc01314 SMc01318 SMc01319 SMc01320 SMc01321 SMc01369 SMc01803 SMc01804 SMc02101 SMc02692 SMc03770 SMc03772 SMc03859 SMc03863 SMc03881 SMc03990...”

bsr5117 50S ribosomal protein L33 from Bradyrhizobium japonicum USDA 110
54% identity, 87% coverage

• Effect of soybean coumestrol on Bradyrhizobium japonicum nodulation ability, biofilm formation, and transcriptional profile
  Lee, Applied and environmental microbiology 2012
  • “...inhibition. Six ribosomal protein genes (blr0420, bll5378, bsr8096, bsr5117, bsr7117, and blr0365) were also downregulated (see Table S2). It has been reported...”

Atu1299 50S ribosomal protein L33 from Agrobacterium tumefaciens str. C58 (Cereon)
54% identity, 87% coverage

• Deep sequencing uncovers numerous small RNAs on all four replicons of the plant pathogen Agrobacterium tumefaciens
  Wilms, RNA biology 2012
  • “...- 69 50 C5 1275442 1275296 - atu1287 146 140 C6 1288585 1288698 atu1298 / atu1299 - 113 100 C7 1345809 1345652 atu1350 / atu1351 - 157, 103 160, 105 C8 1995974 1995854 atu2036 / atu2038 - 120 120 C9 2087200 2087380 atu2122 / atu2123 -...”

BAB2_0631 Ribosomal protein L33 from Brucella melitensis biovar Abortus 2308
56% identity, 87% coverage

• Intracellular adaptation of Brucella abortus
  Lamontagne, Journal of proteome research 2009
  • “...synthesis RluD 7 BAB1_0090 Central carbon metab AcnA 7 BAB1_1150 Central carbon metab Ace 7 BAB2_0631 Protein synthesis LSU L33 8 BAB1_0246 Central carbon metab Gdh 8 BAB2_0938 Central carbon metab Xyl 8 BAB2_0635 Protein synthesis VacB 9 BAB1_0660 Central carbon metab Omp2b 9 BAB2_0547 Central...”

MAB_0333c 50S ribosomal protein L33 from Mycobacterium abscessus ATCC 19977
45% identity, 91% coverage

• Mycobacterium abscessus extracellular vesicles increase mycobacterial resistance to clarithromycin in vitro
  Vermeire, Proteomics 2024 (secret)
• 2-Aminoimidazoles Inhibit Mycobacterium abscessus Biofilms in a Zinc-Dependent Manner
  Belardinelli, International journal of molecular sciences 2022
  • “...with an asterisk. Similarly colored genes denote gene clusters likely to be cotranscribed. MAB_0331c, MAB_0332c, MAB_0333c, MAB_0334c and MAB_0336 are Zn-independent alternative ribosomal proteins. MAB_0335 is likely to be involved in cobalamin biosynthesis. MAB_0575c-MAB_0576c-MAB_0577c encode a putative zinc importer of the ABC-transporter family. The operon encompassing...”
  • “...S18 RpsR2 Zn-independent ribosomal proteins 8.04 9.31 MAB_0332c 30S ribosomal protein S14 RpsN2 7.76 8.93 MAB_0333c 50S ribosomal protein L33 RpmG1 9.72 6.26 MAB_0334c * 50S ribosomal protein L28 RpmB2 9.30 7.83 MAB_0335 * Probable cobalamin synthesis protein Cobalamin biosynthesis 7.95 10.46 MAB_0336 50S ribosomal protein...”

6xywAC / Q9SQT5 6xywAC (see paper)
49% identity, 92% coverage

• Ligand: rna (6xywAC)

AT5G18790 ribosomal protein L33 family protein from Arabidopsis thaliana
49% identity, 81% coverage

• FIONA1-mediated methylation of the 3'UTR of FLC affects FLC transcript levels and flowering in Arabidopsis
  Sun, PLoS genetics 2022
  • “...Orthologous group 212 AT2G18050 fio1-1 fio1-5 HIS1-3, histone H1-3 AT2G40480 fio1-1 fio1-5 no symbol available AT5G18790 fio1-1 fio1-5 no symbol available AT5G56860 fio1-1 fio1-5 GNC, GATA21, GATA TRANSCRIPTION FACTOR 21 AT5G64860 fio1-1 fio1-5 AtDPE1, DPE1, disproportionating enzyme AT1G50250 fio1-1 fio1-2 FTSH1, FTSH protease 1 AT1G52400 fio1-1...”
• Mediator of tolerance to abiotic stress ERF6 regulates susceptibility of Arabidopsis to Meloidogyne incognita
  Warmerdam, Molecular plant pathology 2019
  • “...139:210 4 4.62 At5G18740 At5G18700, At5G18710, At5G18720, At5G18730, At5G18740, At5G18748, At5G18750, At5G18755, At5G18760, At5G18770, At5G18780, At5G18790, At5G187800, At5G18810, At5G18820 6253982 C:T 202:147 4.7 4.84 NA 6261603 A:T 109:240 4.5 4.88 At5G18770 6263591 A:T 139:210 6.1 5.31 At5G18780 6263577 A:T 139:210 6.1 5.31 At5G18780 6263644 A:T 140:209...”
• An Update on Mitochondrial Ribosome Biology: The Plant Mitoribosome in the Spotlight
  Tomal, Cells 2019
  • “...AT4G23620 AT5G66860 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 )...”
• Dynamic modeling of transcriptional gene regulatory network uncovers distinct pathways during the onset of Arabidopsis leaf senescence
  Mishra, NPJ systems biology and applications 2018
  • “...AT1G71520 and its downstream genes ELI3 , AT3G11560 , AT3G02160 , Rap2.6 , ATEXO70H4 , AT5G18790 , and ELF6 at the indicated time points in Col-0 To simulate the impact of transcriptional activities on their target genes, we performed SQUAD simulations on an integrated network that...”

NCgl0833 50S ribosomal protein L33 from Corynebacterium glutamicum ATCC 13032
cg0990 50S ribosomal protein L33 from Corynebacterium glutamicum ATCC 13032
47% identity, 91% coverage

• Transcriptome analysis of Corynebacterium glutamicum in the process of recombinant protein expression in bioreactors
  Sun, PloS one 2017
  • “...regulation, and 5 genes had no gene annotation; thus, the other 4 DEGs (NCgl0487, NCgl0909, NCgl0833 and NCgl0303) were further analyzed. NCgl0487, encoding the 50S ribosomal protein L3 (rplC), was almost 95-fold down-regulated. rplC is a ribosomal protein involved in the translation elongation process, and its...”
  • “...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 two genes (NCgl0303, NCgl1526) up-regulated...”
• 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
  • “...0.58 rpsS 30S ribosomal protein S19 J cg0637 0.55 betB betaine aldehyde dehydrogenase oxireductase C cg0990 0.65 rpmG 50S ribosomal protein L33 J cg1062 0.43 urtB ABC-type urea transport system, permease component E cg1064 0.65 urtC ABC-type urea transport system, permease component E cg1341 0.62 narI...”

MAP3769c RpmG from Mycobacterium avium subsp. paratuberculosis str. k10
43% identity, 91% coverage

• Critical Role of Zur and SmtB in Zinc Homeostasis of Mycobacterium smegmatis
  Goethe, mSystems 2020
  • “...MSMEG_6066 Rv2056c (72.3) MAP3768c (75.2) <0.0001 279.8 30S ribosomal protein S14 rpmG MSMEG_6067 Rv2057c (87.0) MAP3769c (92.6) <0.0001 1,043.5 50S ribosomal protein L33 rpmB MSMEG_6068 Rv2058c (82.1) <0.0001 449.65 50S ribosomal protein L28 MSMEG_6069 Rv0106 (62.1) MAP3770 (57.8) <0.0001 406.31 (4,524.0) CobW/P47K domain-containing protein, MPY recruitment...”
  • “...(72.3) MAP3768c (75.2) 1.00 5778.50 279.80 3,983.5 30S ribosomal protein S14 rpmG MSMEG_6067 Rv2057c (87.0) MAP3769c (92.6) 1.00 5856.67 1043.50 5,015.0 50S ribosomal protein L33 rpmB *MSMEG_6068 Rv2058c (82.1) 1.00 5372.69 449.65 4,055.32 50S ribosomal protein L28 *MSMEG_6069 Rv0106 (62.1) MAP3770 (57.8) 1.00 3492.00 406.31 4,340.00...”
• Identification of a lineage specific zinc responsive genomic island in Mycobacterium avium ssp. paratuberculosis
  Eckelt, BMC genomics 2014
  • “...b Zur box c MAP3778 236 TGATAATGAAAATGATTTTCGTTA MAP3772c 30 CGTTAATGAAAATGATTATCATTA MAP3770 88 GCTTATTGAAAATGATTTTCGACA 33 TCGAGATGAAAATGATTCCCAATA MAP3769c rpmG 283 TCTTGTCGAAAATCATTTTCAATA 338 CCTTATTGGGAATCATTTTCATCT MAP3765 270 GCTTACTGAAAATGATTGTTATTA 139 TGTTAACGAAAATCGTTTTCAGTA MAP3764c pks2 307 GTTTACTGAAAACGATTTTCGTTA MAP3747c cobW 88 GCTTATTGAAAACGATTTTCGACA 33 GCTAGATGAAAACGATTGTCGATA MAP3740 sidA 118 CGACAATGAAAATCGTTTTCAGTA MAP3739c sidG 21 CCTTACTGAAAACGATTTTCATTG MAP3737 197...”

MAV_4876 50S ribosomal protein L33 from Mycobacterium avium 104
41% identity, 91% coverage

• Identification of a lineage specific zinc responsive genomic island in Mycobacterium avium ssp. paratuberculosis
  Eckelt, BMC genomics 2014
  • “...(66.1) MAV_4874 (73.5) <0.0001 218.07 cobW-like cobalamin synthesis, metal chaperone R rpmG *MAP3769c Rv2057c (85.2) MAV_4876 (93.5) <0.0001 191.92 50s ribosomal protein L33 J rpsN2 MAP3768c Rv2056c (81.2) - <0.0001 194.0 30S ribosomal protein S14 RpsN2 J rpsR2 MAP3767c Rv2055c (77.2) MAV_0076 (84.61) 1.0 22.32 #...”

MSMEG_6067 ribosomal protein L33 from Mycobacterium smegmatis str. MC2 155
41% identity, 91% coverage

• Critical Role of Zur and SmtB in Zinc Homeostasis of Mycobacterium smegmatis
  Goethe, mSystems 2020
  • “...protein S18 rpsN MSMEG_6066 Rv2056c (72.3) MAP3768c (75.2) <0.0001 279.8 30S ribosomal protein S14 rpmG MSMEG_6067 Rv2057c (87.0) MAP3769c (92.6) <0.0001 1,043.5 50S ribosomal protein L33 rpmB MSMEG_6068 Rv2058c (82.1) <0.0001 449.65 50S ribosomal protein L28 MSMEG_6069 Rv0106 (62.1) MAP3770 (57.8) <0.0001 406.31 (4,524.0) CobW/P47K domain-containing...”
  • “...genes encoding zinc-independent alternative ribosomal proteins (ARPs) RpsR, RpsN, RpmG, RpmB, and RpmE2 (MSMEG_6065, MSMEG_6066, MSMEG_6067, MSMEG_6068, MSMEG_6070), a gene encoding the porin MspD (MSMEG_6057), and two genes of unknown function (MSMEG_6055, MSMEG_6064). In addition, 7-fold-lower expression upon TPEN treatment was observed for the cobalt-zinc-cadmium resistance...”
• Gene Expression, Bacteria Viability and Survivability Following Spray Drying of Mycobacterium smegmatis
  Lauten, Materials (Basel, Switzerland) 2010
  • “...L32 rpmF 1.1 11.1 0.010 22% MSMEG_6070 ribosomal protein L31 rpmE 0.0 10.1 0.704 0% MSMEG_6067 ribosomal protein L33 rpmG -0.4 9.4 0.368 0% MSMEG_1339 ribosomal protein L33 rpmG 0.6 11.6 0.045 9% MSMEG_6946 ribosomal protein L34 rpmH 0.3 11.5 0.282 0% MSMEG_3792 ribosomal protein L35...”

6z1pAE / Q22L35 6z1pAE (see paper)
47% identity, 81% coverage

• Ligand: rna (6z1pAE)

SCO3428 50S ribosomal protein L33 from Streptomyces coelicolor A3(2)
41% identity, 91% coverage

• The frontline antibiotic vancomycin induces a zinc starvation response in bacteria by binding to Zn(II)
  Zarkan, Scientific reports 2016
  • “...b ) the putative Zur regulated genes SGR5019 (SCO2505 orthologue), SGR0545 (SCO3429 orthologue) and SGR0546 (SCO3428 orthologue) in S. griseus ( c ) the putative Zur regulated genes SSGG01683 (SCO2505 orthologue), SSGG00253 (SCO0476 orthologue) and SSGG06641 (SCO3428 orthologue) in S. roseosporus ( d ) znuA ,...”
• Comparative genomics of Streptomyces avermitilis, Streptomyces cattleya, Streptomyces maritimus and Kitasatospora aureofaciens using a Streptomyces coelicolor microarray system
  Hsiao, Antonie van Leeuwenhoek 2008
  • “...protein 0.39 0.31 0.23 0.89 SCO3427 putative 50S ribosomal protein L31 0.24 0.37 0.22 0.60 SCO3428 putative 50S ribosomal protein L33 0.15 0.28 0.54 0.09 SCO3429 putative 50S ribosomal protein L28 0.68 0.16 0.55 0.45 SCO3430 putative 30S ribosomal protein S14 0.80 0.10 0.17 0.19 SCO3880...”
• The zinc-responsive regulator Zur controls a zinc uptake system and some ribosomal proteins in Streptomyces coelicolor A3(2)
  Shin, Journal of bacteriology 2007
  • “...SCO5359 SCO3427 SCO1150 R Zur NDd L33 rpmG1 rpmG2 rpmG3 SCO4635 SCO3428 SCO0570 NDd Zur R a For the numbering of paralogues, we used the number 1 for those that...”
  • “...coelicolor database ScoDB (http://Streptomyces.org.uk). b The rpmG2 (SCO3428) and rpmE2 (SCO3427) genes are cotranscribed from the rpmG2 promoter. c , present;...”
• Zinc-responsive regulation of alternative ribosomal protein genes in Streptomyces coelicolor involves zur and sigmaR
  Owen, Journal of bacteriology 2007
  • “...rpmE2 (SCO3427) rpmE3 (SCO1150) rpmF2 (SCO0436) rpmG2 (SCO3428) rpmG3 (SCO0570) rpmJ2 (SCO0569) gation from E. coli ET12567(pUZ8002) (24). A single-crossover...”
• New pleiotropic effects of eliminating a rare tRNA from Streptomyces coelicolor, revealed by combined proteomic and transcriptomic analysis of liquid cultures
  Hesketh, BMC genomics 2007
  • “...SCO3285 large gly/ala rich protein 7.72E-03 N/A up SCO3286 secreted protein 0.00772 0.05 up Secreted SCO3428 50S ribosomal protein N/A 0.082* down Predicted pI = 10.8, mwt = 6416 Da SCO3608 hypothetical protein N/A 0.1* up Predicted 3 transmembrane domains SCO3717 probable cation transport system component...”

9b0016 / P35871 9b0016 (see paper)
40% identity, 94% coverage

• Ligands: rna; magnesium ion; zinc ion (9b0016)

RL33_THET8 / P35871 Large ribosomal subunit protein bL33; 50S ribosomal protein L33 from Thermus thermophilus (strain ATCC 27634 / DSM 579 / HB8) (see paper)
TTHA0250 50S ribosomal protein L33 from Thermus thermophilus HB8
40% identity, 93% coverage

• function: Found on the solvent side of the large subunit
  function: Contacts the E site tRNA
  subunit: Part of the 50S ribosomal subunit
• Determination and Dissection of DNA-Binding Specificity for the Thermus thermophilus HB8 Transcriptional Regulator TTHB099
  Moncja, International journal of molecular sciences 2020
  • “...transporter +2.300 9.53 10 4 1 TTHA0251 Elongation factor Tu 1.254 1.17 10 2 1 TTHA0250 50S ribosomal protein L33 1.139 8.04 10 3 2 TTHA0249 Preprotein translocase subunit SecE 0.997 9.18 10 3 3 TTHA0248 Transcription antitermination protein NusG 1.136 7.86 10 3 1 TTHA0247...”
• Lysine propionylation is a prevalent post-translational modification in Thermus thermophilus
  Okanishi, Molecular & cellular proteomics : MCP 2014
  • “...Translation TTHA0142 TTHA0161 TTHA0162 TTHA0210 TTHA0246 TTHA0250 TTHA0251 TTHA0366 TTHA0543 TTHA0551 TTHA0712 TTHA0858 TTHA0860 TTHA0875 TTHA1067 TTHA1125...”
• A Transfer Learning-Based Approach for Lysine Propionylation Prediction
  Li, Frontiers in physiology 2021
  • “...protein L5 (rplE) P80377 30S ribosomal protein S13 (rpsM) Q5SHN3 30S ribosomal protein S12 (rpsL) P35871 50S ribosomal protein L33 (rpmG) Q8VVE2 50S ribosomal protein L7/L12 (rplL) Q5SLY1 30S ribosomal protein S1 (rpsA) P17291 30S ribosomal protein S7 (TTHA1696) Q9Z9H5 50S ribosomal protein L17 (rplQ) Bold...”

LACR_0076 Ribosomal protein L33 from Lactococcus lactis subsp. cremoris SK11
47% identity, 96% coverage

• Surface proteome analysis of a natural isolate of Lactococcus lactis reveals the presence of pili able to bind human intestinal epithelial cells
  Meyrand, Molecular & cellular proteomics : MCP 2013
  • “...LLKF_1334 LACR_2596 LL2098 LACR_2386 LACR_2583 LACR_0076 LACR_1387 LACR_0246 LACR_2400 LACR_1182 LACR_2377 llmg_2383 LACR_1180 LACR_0077 LL2191 LACR_2054...”

5dm61 / Q9RSS4 Crystal structure of the 50s ribosomal subunit from deinococcus radiodurans (see paper)
55% identity, 61% coverage

• Ligand: rna (5dm61)

A4VT05 Large ribosomal subunit protein bL33 from Streptococcus suis (strain 05ZYH33)
SSU05_0276 50S ribosomal protein L33 from Streptococcus suis 05ZYH33
STER_RS09560 50S ribosomal protein L33 from Streptococcus thermophilus LMD-9
43% identity, 96% coverage

• DivIVA Interacts with the Cell Wall Hydrolase MltG To Regulate Peptidoglycan Synthesis in Streptococcus suis
  Jiang, Microbiology spectrum 2023
  • “...Predicted periplasmic solute-binding protein 25.175 1.6981 + A4VTI3 SSU05_0456 Superfamily II helicase 13.908 1.6915 + A4VT05 SSU05_0276 rpmG 50S ribosomal protein L33 5.9249 1.6104 + A4VU28 SSU05_0651 murE UDP- N -acetylmuramoyl- l -alanyl- d -glutamate- l -lysine ligase 53.209 1.6102 + A4VX26 SSU05_1699 Pseudouridine synthase 27.371...”
• DivIVA Interacts with the Cell Wall Hydrolase MltG To Regulate Peptidoglycan Synthesis in Streptococcus suis
  Jiang, Microbiology spectrum 2023
  • “...periplasmic solute-binding protein 25.175 1.6981 + A4VTI3 SSU05_0456 Superfamily II helicase 13.908 1.6915 + A4VT05 SSU05_0276 rpmG 50S ribosomal protein L33 5.9249 1.6104 + A4VU28 SSU05_0651 murE UDP- N -acetylmuramoyl- l -alanyl- d -glutamate- l -lysine ligase 53.209 1.6102 + A4VX26 SSU05_1699 Pseudouridine synthase 27.371 1.5572...”
• Cell Proteins Obtained by Peptic Shaving of Two Phenotypically Different Strains of Streptococcus thermophilus as a Source of Anti-Inflammatory Peptides
  Allouche, Nutrients 2022
  • “...88.53 9 44.26 STER_1953|ID:1899670|rpmF| STER_RS09555 50S ribosomal subunit protein L32 6.78 Cyto 12 83.61 STER_1954|ID:1899671|rpmG| STER_RS09560 50S ribosomal subunit protein L33 5.92 Cyto 19 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...”

CT150 L33 Ribosomal Protein from Chlamydia trachomatis D/UW-3/CX
46% identity, 92% coverage

• Chlamydia trachomatis infection induces replication of latent HHV-6
  Prusty, PloS one 2013
  • “...ND ND (<5) 52664.978 ND 11 CT159 64 ND ND ND (<5) 2382.5124 ND 12 CT150 128 ND ND ND (<5) 65655.5437 ND 13 CT152 <32 ND ND ND (<5) 1024506.99 ND 14 CT155 <32+/ 160 20 ND (<5) 10184.9924 ND 15 CT179 <32 ND ND...”

SP_RS10895 50S ribosomal protein L33 from Streptococcus pneumoniae TIGR4
P61361 Large ribosomal subunit protein bL33C from Streptococcus pneumoniae (strain ATCC BAA-255 / R6)
SP_2135 50S ribosomal protein L33 from Streptococcus pneumoniae TIGR4
41% identity, 96% coverage

• Streptococcus pneumoniae metal homeostasis alters cellular metabolism
  Burcham, Metallomics : integrated biometal science 2020
  • “...SP_RS04035 tetrahydrafolate dehydrogenase, oxidoreductase activity 25.0 SP1690 SP_RS08350 sugar ABC transporter substrate-binding protein 14.3 RpmG SP_RS10895 50s ribosomal protein L33 12.5 NanB SP_RS08335 neuraminidase B 12.5 PstS2 SP_RS10610 phosphate ABC transporter 10.0 SP1536 SP_RS07565 methyltransferase, TrmN6 10.0 SP1686 SP_RS08330 Gfo/Idh/MocA family oxidoreductase 5.0 AgaS SP_RS00360 tagatose-6-phosphate-isomerase...”
• A Global Genomic Characterization of Nairoviruses Identifies Nine Discrete Genogroups with Distinctive Structural Characteristics and Host-Vector Associations.
  Walker, The American journal of tropical medicine and hygiene 2016
  • “...Saulges, Mayenne, France White-toed shrew ( Crocidura russula ) 72 JF911697 JF911698 JF911699 Keterah (KTRV) P61361 Not assigned Keterah February 11, 1966 Keterah, Kelantan, Malaysia Soft ticks ( Argae pusillus ) from lesser Asian yellow house bat ( Scotophilus kuhlii [ temmincki] ) 73 KR537447 KR537448...”
• Phenotypic, genomic, and transcriptional characterization of Streptococcus pneumoniae interacting with human pharyngeal cells
  Kimaro, BMC genomics 2013
  • “...identified by the microarray experiments: an average of SP_0002 (DNA polymerase), SP_0085 (ribosomal protein) and SP_2135 (ribosomal protein). Each sample of each biological replicate was tested three times. RNA Sequencing The transcriptome of S. pneumoniae TIGR4 adhering to D562 host cells was determined using RNA-Seq on...”

Q9Z8T4 Large ribosomal subunit protein bL33 from Chlamydia pneumoniae
44% identity, 92% 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
  • “...study including L10 (Q9Z9A2), L9 (Q9Z6V3), L4 (Q9Z7Q8), L5 (Q9Z7R9), L29 (Q9Z7R5), L27 (Q9Z807), L33 (Q9Z8T4), L34 (Q9Z6X1) and L35 (Q9Z6R8), L36 (Q9Z6X0), which potentially involved in various steps of translation and ribosome biogenesis in C. pneumoniae . Control of translation is a critical component for...”

IUJ47_RS03245 50S ribosomal protein L33 from Enterococcus faecalis
P59629 Large ribosomal subunit protein bL33D from Enterococcus faecalis (strain ATCC 700802 / V583)
37% identity, 96% coverage

• Antibacterial Components and Modes of the Methanol-Phase Extract from Commelina communis Linn
  Liu, Plants (Basel, Switzerland) 2023
  • “...ribosomal protein L9 IUJ47_RS06135 15.154 50S ribosomal protein L32 IUJ47_RS03240 24.038 30S ribosomal protein S14 IUJ47_RS03245 25.083 50S ribosomal protein L33 Phenylalanine, tyrosine IUJ47_RS10435 0.021 Shikimate dehydrogenase and tryptophan IUJ47_RS10440 0.066 3-deoxy-7-phosphoheptulonate synthase biosynthesis IUJ47_RS11275 0.151 Type I 3-dehydroquinate dehydratase IUJ47_RS10445 0.154 3-dehydroquinate synthase IUJ47_RS10455 0.227...”
• Gliotoxin-mediated bacterial growth inhibition is caused by specific metal ion depletion
  Downes, Scientific reports 2023
  • “...oxidoreductase Unique N/A 12 36.1 H7C719 50S ribosomal protein L33 4 Unique N/A 2 40.8 P59629 Cobalamin synthesis protein/P47K family protein Unique N/A 6 25.6 Q82Z69 30S ribosomal protein S14 1 Unique N/A 1 13.5 Q8KU58 Protein EbsA Unique N/A 3 19 P36920 3-dehydroquinate dehydratase Unique...”
  • “...3 Unique N/A 2 26.5 P59628 50S ribosomal protein L33 4 Unique N/A 3 44.9 P59629 Cobalamin synthesis protein/P47K family protein Unique N/A 6 25.6 Q82Z69 50S ribosomal protein L28 Unique N/A 4 48.4 Q82ZE4 UPF0637 protein EF_3078 Unique N/A 3 26.6 Q82ZH9 Glycosyl transferase, group...”

M6_Spy1835 LSU ribosomal protein L33P from Streptococcus pyogenes MGAS10394
SpyM3_1817 50S ribosomal protein L33 from Streptococcus pyogenes MGAS315
SUB1796 50S ribosomal protein L33 from Streptococcus uberis 0140J
41% identity, 96% 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
  • “...membrane spanning protein M6_Spy1830 1.50 Hypothetical membrane spanning protein M6_Spy1834 1.86 50S ribosomal protein L32 M6_Spy1835 1.67 50S ribosomal protein L33 M6_Spy1842 1.90 Hypothetical protein M6_Spy1846 1.58 Transcriptional regulator, PadR family Table 3 Upregulated genes of S. pyogenes under low shear modeled microgravity with respect to...”
• Novel regulatory small RNAs in Streptococcus pyogenes
  Tesorero, PloS one 2013
  • “...Q, P SSRC41 SPyM3_1798 hypothetical protein <<< SPyM3_1799 transcriptional regulator Spx <<< Q, Z SSRC42 SPyM3_1817 50S ribosomal protein L33 >>> SPyM3_1818 putative cadmium resistance protein >>> Q, Z [40] SSRC43 SPyM3_1822 hypothetical protein >>> SPyM3_1823 hypothetical protein <<< Q, Z SSRC44 SPyM3_1836 hypothetical protein <<<...”
• Discrimination of contagious and environmental strains of Streptococcus uberis in dairy herds by means of mass spectrometry and machine-learning
  Esener, Scientific reports 2018
  • “...S. uberis (Fig. 6 ) showed that 5 out of 8 proteins (SUB14226, SUB0666, SUB0081, SUB1796 and SUB0585) share common first neighbour proteins with each other. Interestingly, SUB0666, SUB0081 and SUB1796 were also found to interact with each other. The ontology functions of these 158 proteins...”
  • “...according to the aspects of biological process, molecular function and cellular component (see Methods). The SUB1796 protein is the ribosomal protein-L33 (RP-L33), a relatively small protein consisting of 49 to 66 amino acids, part of the large ribosomal subunit 21 . In GO, RP-L33 is annotated...”

GSU2870 ribosomal protein L33 from Geobacter sulfurreducens PCA
47% identity, 96% coverage

• Evolution of electron transfer out of the cell: comparative genomics of six Geobacter genomes
  Butler, BMC genomics 2010
  • “...protein L14 39995936 GSU0830 0.92 heavy metal efflux pump 39995264 GSU0153 0.92 argininosuccinate synthase 39997961 GSU2870 0.92 ribosomal protein L33 39995685 GSU0578 0.92 glycyl-tRNA synthetase 39998185 GSU3095 0.92 imidazoleglycerol phosphate synthase 39997958 GSU2867 0.92 ribosomal protein L11 39995210 GSU0099 0.92 MglA protein 39995598 GSU0490 0.92 acetyl-CoA...”

LSEI_1847 Ribosomal protein L33 from Lactobacillus casei ATCC 334
39% identity, 96% coverage

• Physiological and transcriptional response of Lactobacillus casei ATCC 334 to acid stress
  Broadbent, Journal of bacteriology 2010
  • “...LSEI_1642 LSEI_1641 LSEI_1640 LSEI_1644 LSEI_1645 LSEI_1847 LSEI_1572 LSEI_1573 LSEI_1574 LSEI_1575 LSEI_1576 LSEI_1577 LSEI_2272 LSEI_2273 LSEI_2476 LSEI_2478...”

SCO0570 50S ribosomal protein L33 from Streptomyces coelicolor A3(2)
40% identity, 89% coverage

• Transcriptional Response of Streptomyces coelicolor to Rapid Chromosome Relaxation or Long-Term Supercoiling Imbalance
  Szafran, Frontiers in microbiology 2019
  • “...protein sco7221 9 1.64 Polyketide synthase sco7681sco7688 617 1.582.00 Coelibactin synthesis genes Other genes rpmG sco0570 68 1.58 50S ribosomal protein L33 tuf3 sco1321 10 4.60 Elongation factor Tu sco2171 14 1.79 Putative secreted protease ohrA sco2986 2 1.88 Hypothetical protein sco3425 24 1.50 30S ribosomal...”
• Conservation of thiol-oxidative stress responses regulated by SigR orthologues in actinomycetes
  Kim, Molecular microbiology 2012
  • “...a Number b Name Description Confirm c 3 SCO0569 rpmJ 50S ribosomal protein L36 3 SCO0570 * rpmG3 50S ribosomal protein L33 (C-type) (S1) 8 SCO0882 * Hypothetical protein, possible dithiol-disulphide isomerase (S1) 8 SCO0884 * Probable oxidoreductase, probable pyridine nucleotide-disulphide oxidoreductases 1 SCO0885 * trxC...”
• The global role of ppGpp synthesis in morphological differentiation and antibiotic production in Streptomyces coelicolor A3(2)
  Hesketh, Genome biology 2007
  • “...to the majority of ribosomal protein genes (Figure 5a ). The adjacent ribosomal protein gene SCO0570 ( rpmG3 ) encodes an analogous cysteine-less alternative to the RpmG protein, and has a similar pattern of expression to SCO0569 in the parent strain. Although not present in the...”
  • “...genes. (a) Different growth-phase dependent expression of genes encoding the alternative ribosomal proteins SCO0569 and SCO0570 compared to the 50S ribosomal protein genes. In each panel, the x-axis represents culture age, and the y-axis is normalized transcript abundance in log 10 scale. (b) qRT-PCR shows transcription...”
• The zinc-responsive regulator Zur controls a zinc uptake system and some ribosomal proteins in Streptomyces coelicolor A3(2)
  Shin, Journal of bacteriology 2007
  • “...SCO3427 SCO1150 R Zur NDd L33 rpmG1 rpmG2 rpmG3 SCO4635 SCO3428 SCO0570 NDd Zur R a For the numbering of paralogues, we used the number 1 for those that contain...”
  • “...coelicolor genome, rpmG1 (SCO4635), rpmG2 (SCO3428), and rpmG3 (SCO0570). The rpmG1 gene contains a zinc-binding motif, whereas rpmG2 and rpmG3 do not. We...”
• Zinc-responsive regulation of alternative ribosomal protein genes in Streptomyces coelicolor involves zur and sigmaR
  Owen, Journal of bacteriology 2007
  • “...rpmE3 (SCO1150) rpmF2 (SCO0436) rpmG2 (SCO3428) rpmG3 (SCO0570) rpmJ2 (SCO0569) gation from E. coli ET12567(pUZ8002) (24). A single-crossover recombinant was...”

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Statistics

How It Works

PaperBLAST builds a database of protein sequences that are linked to scientific articles. These links come from automated text searches against the articles in EuropePMC and from manually-curated information from GeneRIF, UniProtKB/Swiss-Prot, BRENDA, CAZy (as made available by dbCAN), BioLiP, CharProtDB, MetaCyc, EcoCyc, TCDB, REBASE, the Fitness Browser, and a subset of the European Nucleotide Archive with the /experiment tag. Given this database and a protein sequence query, PaperBLAST uses protein-protein BLAST to find similar sequences with E < 0.001.

To build the database, we query EuropePMC with locus tags, with RefSeq protein identifiers, and with UniProt accessions. We obtain the locus tags from RefSeq or from MicrobesOnline. We use queries of the form "locus_tag AND genus_name" to try to ensure that the paper is actually discussing that gene. Because EuropePMC indexes most recent biomedical papers, even if they are not open access, some of the links may be to papers that you cannot read or that our computers cannot read. We query each of these identifiers that appears in the open access part of EuropePMC, as well as every locus tag that appears in the 500 most-referenced genomes, so that a gene may appear in the PaperBLAST results even though none of the papers that mention it are open access. We also incorporate text-mined links from EuropePMC that link open access articles to UniProt or RefSeq identifiers. (This yields some additional links because EuropePMC uses different heuristics for their text mining than we do.)

For every article that mentions a locus tag, a RefSeq protein identifier, or a UniProt accession, we try to select one or two snippets of text that refer to the protein. If we cannot get access to the full text, we try to select a snippet from the abstract, but unfortunately, unique identifiers such as locus tags are rarely provided in abstracts.

PaperBLAST also incorporates manually-curated protein functions:

• Proteins from NCBI's RefSeq are included if a GeneRIF entry links the gene to an article in PubMed^®. GeneRIF also provides a short summary of the article's claim about the protein, which is shown instead of a snippet.
• Proteins from Swiss-Prot (the curated part of UniProt) are included if the curators identified experimental evidence for the protein's function (evidence code ECO:0000269). For these proteins, the fields of the Swiss-Prot entry that describe the protein's function are shown (with bold headings).
• Proteins from BRENDA, a curated database of enzymes, are included if they are linked to a paper in PubMed and their full sequence is known.
• Every protein from the non-redundant subset of BioLiP, a database of ligand-binding sites and catalytic residues in protein structures, is included. Since BioLiP itself does not include descriptions of the proteins, those are taken from the Protein Data Bank. Descriptions from PDB rely on the original submitter of the structure and cannot be updated by others, so they may be less reliable. (For SitesBLAST and Sites on a Tree, we use a larger subset of BioLiP so that every ligand is represented among a group of structures with similar sequences, but for PaperBLAST, we use the non-redundant set provided by BioLiP.)
• Every protein from EcoCyc, a curated database of the proteins in Escherichia coli K-12, is included, regardless of whether they are characterized or not.
• Proteins from the MetaCyc metabolic pathway database are included if they are linked to a paper in PubMed and their full sequence is known.
• Proteins from the Transport Classification Database (TCDB) are included if they have known substrate(s), have reference(s), and are not described as uncharacterized or putative. (Some of the references are not visible on the PaperBLAST web site.)
• Every protein from CharProtDB, a database of experimentally characterized protein annotations, is included.
• Proteins from the CAZy database of carbohydrate-active enzymes are included if they are associated with an Enzyme Classification number. Even though CAZy does not provide links from individual protein sequences to papers, these should all be experimentally-characterized proteins.
• Proteins from the REBASE database of restriction enzymes are included if they have known specificity.
• Every protein with an evidence-based reannotation (based on mutant phenotypes) in the Fitness Browser is included.
• Sequence-specific transcription factors (including sigma factors and DNA-binding response regulators) with experimentally-determined DNA binding sites from the PRODORIC database of gene regulation in prokaryotes.
• Putative transcription factors from RegPrecise that have manually-curated predictions for their binding sites. These predictions are based on conserved putative regulatory sites across genomes that contain similar transcription factors, so PaperBLAST clusters the TFs at 70% identity and retains just one member of each cluster.
• Coding sequence (CDS) features from the European Nucleotide Archive (ENA) are included if the /experiment tag is set (implying that there is experimental evidence for the annotation), the nucleotide entry links to paper(s) in PubMed, and the nucleotide entry is from the STD data class (implying that these are targeted annotated sequences, not from shotgun sequencing). Also, to filter out genes whose transcription or translation was detected, but whose function was not studied, nucleotide entries or papers with more than 25 such proteins are excluded. Descriptions from ENA rely on the original submitter of the sequence and cannot be updated by others, so they may be less reliable.

Except for GeneRIF and ENA, the curated entries include a short curated description of the protein's function. For entries from BioLiP, the protein's function may not be known beyond binding to the ligand. Many of these entries also link to articles in PubMed.

For more information see the PaperBLAST paper (mSystems 2017) or the code. You can download PaperBLAST's database here.

Changes to PaperBLAST since the paper was written:

• November 2023: incorporated PRODORIC and RegPrecise. Many PRODORIC entries were not linked to a protein sequence (no UniProt identifier), so we added this information.
• February 2023: BioLiP changed their download format. PaperBLAST now includes their non-redundant subset. SitesBLAST and Sites on a Tree use a larger non-redundant subset that ensures that every ligand is represented within each cluster. This should ensure that every binding site is represented.
• June 2022: incorporated some coding sequences from ENA with the /experiment tag.
• March 2022: incorporated BioLiP.
• April 2020: incorporated TCDB.
• April 2019: EuropePMC now returns table entries in their search results. This has expanded PaperBLAST's database, but most of the new entries are of low relevance, and the resulting snippets are often just lists of locus tags with annotations.
• February 2018: the alignment page reports the conservation of the hit's functional sites (if available from from Swiss-Prot or UniProt)
• January 2018: incorporated BRENDA.
• December 2017: incorporated MetaCyc, CharProtDB, CAZy, REBASE, and the reannotations from the Fitness Browser.
• September 2017: EuropePMC no longer returns some table entries in their search results. This has shrunk PaperBLAST's database, but has also reduced the number of low-relevance hits.

Many of these changes are described in Interactive tools for functional annotation of bacterial genomes.

Secrets

PaperBLAST cannot provide snippets for many of the papers that are published in non-open-access journals. This limitation applies even if the paper is marked as "free" on the publisher's web site and is available in PubmedCentral or EuropePMC. If a journal that you publish in is marked as "secret," please consider publishing elsewhere.

Omissions from the PaperBLAST Database

Many important articles are missing from PaperBLAST, either because the article's full text is not in EuropePMC (as for many older articles), or because the paper does not mention a protein identifier such as a locus tag, or because of PaperBLAST's heuristics. If you notice an article that characterizes a protein's function but is missing from PaperBLAST, please notify the curators at UniProt or add an entry to GeneRIF. Entries in either of these databases will eventually be incorporated into PaperBLAST. Note that to add an entry to UniProt, you will need to find the UniProt identifier for the protein. If the protein is not already in UniProt, you can ask them to create an entry. To add an entry to GeneRIF, you will need an NCBI Gene identifier, but unfortunately many prokaryotic proteins in RefSeq do not have corresponding Gene identifers.

References

PaperBLAST: Text-mining papers for information about homologs.
M. N. Price and A. P. Arkin (2017). mSystems, 10.1128/mSystems.00039-17.

Europe PMC in 2017.
M. Levchenko et al (2017). Nucleic Acids Research, 10.1093/nar/gkx1005.

Gene indexing: characterization and analysis of NLM's GeneRIFs.
J. A. Mitchell et al (2003). AMIA Annu Symp Proc 2003:460-464.

UniProt: the universal protein knowledgebase.
The UniProt Consortium (2016). Nucleic Acids Research, 10.1093/nar/gkw1099.

BRENDA in 2017: new perspectives and new tools in BRENDA.
S. Placzek et al (2017). Nucleic Acids Research, 10.1093/nar/gkw952.

The EcoCyc database: reflecting new knowledge about Escherichia coli K-12.
I. M. Keeseler et al (2016). Nucleic Acids Research, 10.1093/nar/gkw1003.

The MetaCyc database of metabolic pathways and enzymes.
R. Caspi et al (2018). Nucleic Acids Research, 10.1093/nar/gkx935.

CharProtDB: a database of experimentally characterized protein annotations.
R. Madupu et al (2012). Nucleic Acids Research, 10.1093/nar/gkr1133.

The carbohydrate-active enzymes database (CAZy) in 2013.
V. Lombard et al (2014). Nucleic Acids Research, 10.1093/nar/gkt1178.

The Transporter Classification Database (TCDB): recent advances
M. H. Saier, Jr. et al (2016). Nucleic Acids Research, 10.1093/nar/gkv1103.

REBASE - a database for DNA restriction and modification: enzymes, genes and genomes.
R. J. Roberts et al (2015). Nucleic Acids Research, 10.1093/nar/gku1046.

Deep annotation of protein function across diverse bacteria from mutant phenotypes.
M. N. Price et al (2016). bioRxiv, 10.1101/072470.