PaperBLAST
PaperBLAST Hits for sp|B1VAE8|RL3_PHYAS Large ribosomal subunit protein uL3 OS=Phytoplasma australiense OX=59748 GN=rplC PE=3 SV=1 (221 a.a., MAQGILGKKI...)
Show query sequence
>sp|B1VAE8|RL3_PHYAS Large ribosomal subunit protein uL3 OS=Phytoplasma australiense OX=59748 GN=rplC PE=3 SV=1
MAQGILGKKIGMTQMFNEQGEIIPITIVDVSANVVLQQKNVAIDGYNATQIGFDDKKDKI
TTKPMLGHFKKAKTTPKRFIKEIIFKKENISSLSALAVGDQVSCDLFQVGDLVDVTGTSK
GKGFAGVIKRHNQSRGPETHGSRHHRRPGSMGPIKGKIKGKKLPGQMGHQTVTIQNLVLF
SVDNQKNLFLIKGSVPGPNKGFVVIKSAVKKLSKEQANAKI
Running BLASTp...
Found 141 similar proteins in the literature:
BC_0131 50S ribosomal protein L3 from Bacillus cereus ATCC 14579
58% identity, 95% coverage
RL3_BACSU / P42920 Large ribosomal subunit protein uL3; 50S ribosomal protein L3; BL3 from Bacillus subtilis (strain 168) (see 3 papers)
BSU01160 50S ribosomal protein L3 from Bacillus subtilis subsp. subtilis str. 168
NP_387997 ribosomal protein L3 (BL3) from Bacillus subtilis subsp. subtilis str. 168
55% identity, 95% coverage
- function: One of the primary rRNA binding proteins, it binds directly near the 3'-end of the 23S rRNA, where it nucleates assembly of the 50S subunit (By similarity). Strongly stimulates 23S rRNA precursor processing by mini-ribonuclease 3 (MrnC); 20-30% DMSO can replace L3, suggesting the protein may alter rRNA conformation.
subunit: Part of the 50S ribosomal subunit (PubMed:30126986). Forms a cluster with proteins L14 and L19 (By similarity). Interacts with RNA helicase CshA (PubMed:23175651). - The Blueprint of a Minimal Cell: MiniBacillus
Reuß, Microbiology and molecular biology reviews : MMBR 2016 - “...synthetase (major) Valyl-tRNA synthetase BSU01030 BSU01190 BSU01160 BSU01170 BSU01280 BSU01310 BSU40500 BSU01040 BSU01020 BSU01050 BSU01490 BSU01260 BSU01350...”
- Single mutations introduced in the essential ribosomal proteins L3 and S10 cause a sporulation defect in Bacillus subtilis.
Akanuma, The Journal of general and applied microbiology 2013 (PubMed)- GeneRIF: Mutant cells harboring the G52D mutation in the L3 ribosomal protein accumulated 30S subunit at 45 degrees C, probably due to a defect in 50S formation, and exhibited a reduction in the sporulation frequency at high temperature.
- Ribosomal protein L3 bound to 23S precursor rRNA stimulates its maturation by Mini-III ribonuclease.
Redko, Molecular microbiology 2009 (PubMed)- GeneRIF: Stimulation of the Mini-III ribonuclease cleavage reaction is through L3 binding to its normal site at the 3' end of 23S rRNA.
- Proteomics analyses of Bacillus subtilis after treatment with plumbagin, a plant-derived naphthoquinone
Reddy, Omics : a journal of integrative biology 2015 - “...protein L17 OS P05657 50S ribosomal protein L27 OS P42920 50S ribosomal protein L3 OS P19947 50S ribosomal protein L30 OS O34967 50S ribosomal protein L31 type...”
- Interactions of an essential Bacillus subtilis GTPase, YsxC, with ribosomes
Wicker-Planquart, Journal of bacteriology 2008 - “...L27 (RL27_BACSU) L7/L12 (RL7_BACSU) L23 (RL23_BACSU) Q06797 P42920 P42920 Q06797 P42923 P46898 P05657 P02394 P42924 762.4 92.4 722.9 542.3 401.4 69.6...”
SPV_0193 50S ribosomal protein L3 from Streptococcus pneumoniae
SP_0209 50S ribosomal protein L3 from Streptococcus pneumoniae TIGR4
spr0188 50S Ribosomal protein L3 from Streptococcus pneumoniae R6
SPD_0193 ribosomal protein L3 from Streptococcus pneumoniae D39
58% identity, 95% coverage
- Refining the Pneumococcal Competence Regulon by RNA Sequencing
Slager, Journal of bacteriology 2019 - “...fold change at: 3 min 10 min 20 min SPV_0192 rpsJ 4,585 0.7 0.0 0.1 SPV_0193 rplC 2,992 0.9 0.1 0.0 SPV_0194 rplD 2,181 0.8 0.1 0.3 SPV_0195 rplW 2,919 1.0 0.2 0.2 SPV_0196 rplB 2,611 1.0 0.2 0.1 SPV_0197 rpsS 4,134 1.0 0.5 0.1 SPV_0198...”
- The Streptococcus pneumoniae transcriptome in patient cerebrospinal fluid identifies novel virulence factors required for meningitis
Wall, 2024 - Biofilm and planktonic pneumococci demonstrate disparate immunoreactivity to human convalescent sera
Sanchez, BMC microbiology 2011 - “...9 28 50S ribosomal protein L2 rplB (SP_0212) 0 7 50S ribosomal protein L3 rplC (SP_0209) 0 4 50S ribosomal protein L4 rplD (SP_0210) 5 11 50S ribosomal protein L5 rplE (SP_0221) 10 23 50S ribosomal protein L6 rplF SP_0225 6 5 50S ribosomal protein L7/L12...”
- Antimicrobial resistance and virulence: a successful or deleterious association in the bacterial world?
Beceiro, Clinical microbiology reviews 2013 - “...the 23S rRNA gene and mutations in spr0188 (50S ribosomal protein L3), spr01887 (ABC transporter ATP-binding/ membrane-spanning protein), and spr0333 (conserved...”
- Whole genome analysis of linezolid resistance in Streptococcus pneumoniae reveals resistance and compensatory mutations
Billal, BMC genomics 2011 - “...of colonies tested spr_ rrnaD d spr_ rrnaC d spr_ rrnaB d spr_ rrnaA d spr0188 e spr0196 f spr1021 g R6 0.5 4 W W W W W W W R6T1 8 4 M W W M W W W R6T2 16 4 M M...”
- “...mutation in the four copies of spr_rrna23S. e Mutant 1974M1 had a T409C mutation in spr0188. f Mutant 1974M1 had a A235G mutation in spr0196. g Mutant 1974M1 had a G-29T mutation in spr1021 (the number preceded by '-' indicates the position upstream of the ATG)....”
- Transcriptional regulation and signature patterns revealed by microarray analyses of Streptococcus pneumoniae R6 challenged with sublethal concentrations of translation inhibitors
Ng, Journal of bacteriology 2003 - “...fold changea Cmb Purb Tetb spr0078 spr0187 spr0188 spr0189 spr0190 spr0191 spr0192 spr0194 spr0196 spr0197 spr0200 spr0201 spr0204 spr0205 spr0555 spr0682...”
- The Rgg1518 transcriptional regulator is a necessary facet of sugar metabolism and virulence in Streptococcus pneumoniae
Shlla, Molecular microbiology 2021 - “...to be part of an operon including SPD_0315, SPD_1053, SPD_1634, SPD_1342, SPD_1461, SPD_1127, SPD_0113, SPD_0122, SPD_0193, SPD_0197, SPD_0208, SPD_0126, SPD_0341, SPD_0378, SPD_0404 and SPD_1512. The genetic fragment containing the putative promoter sites of target genes were amplified using primers containing 5-FAM fluorescent tags ( STable 4...”
7aqcD / P42920 Structure of the bacterial rqc complex (decoding state) (see paper)
55% identity, 94% coverage
V6YZ47 Large ribosomal subunit protein uL3 from Streptococcus agalactiae LMG 14747
57% identity, 95% coverage
llmg_2383 50S ribosomal protein L3 from Lactococcus lactis subsp. cremoris MG1363
56% identity, 95% coverage
IUJ47_RS04525 50S ribosomal protein L3 from Enterococcus faecalis
57% identity, 95% coverage
SMU_RS09255 50S ribosomal protein L3 from Streptococcus mutans UA159
56% identity, 95% coverage
5myjBE / A2RNQ5 of 70S ribosome from Lactococcus lactis (see paper)
56% identity, 95% coverage
lmo2632 ribosomal protein L3 from Listeria monocytogenes EGD-e
56% identity, 95% coverage
7nhkH / A0A1B4XKR3 7nhkH (see paper)
57% identity, 94% coverage
8a57H / Q8Y440 Cryo-em structure of hflxr bound to the listeria monocytogenes 50s ribosomal subunit. (see paper)
56% identity, 94% coverage
BB562_12100 50S ribosomal protein L3 from Lactiplantibacillus pentosus
56% identity, 94% coverage
- Transcriptomic Profile and Probiotic Properties of Lactiplantibacillus pentosus Pre-adapted to Edible Oils
Alonso, Frontiers in microbiology 2021 - “...BB562_12025, BB562_12030, BB562_12035, BB562_12040, BB562_12045, BB562_12050, BB562_12055, BB562_12060, BB562_12065, BB562_12070, BB562_12080, BB562_12085, BB562_12090, BB562_12095, and BB562_12100), and the genes encoding 30S and 50S ribosomal proteins involved in nucleic acid and protein synthesis were down-regulated ( Supplementary Table 1 and Supplementary Figure 2 ). With respect to...”
IVR12_00778 50S ribosomal protein L3 from Limosilactobacillus reuteri
54% identity, 97% coverage
- Recombinant Limosilactobacillus (Lactobacillus) delivering nanobodies against Clostridium perfringens NetB and alpha toxin confers potential protection from necrotic enteritis
Gangaiah, MicrobiologyOpen 2022 - “...ribosomal protein L19 IVR12_02459 15 99 ValinetRNA ligase IVR12_01849 102 98 50S ribosomal protein L3 IVR12_00778 24 95 Putative aminoacid ABC transporterbinding protein precursor IVR12_01610 29 86 Arabinogalactan endo1,4betagalactosidase precursor IVR12_00642 166 85 Maltose phosphorylase IVR12_01307 87 85 GTPbinding protein TypA/BipA IVR12_00521 69 85 Chaperone protein...”
- “...Glucose6phosphate 1dehydrogenase IVR12_01053 56 283 Elongation factor Ts IVR12_00463 32 278 50S ribosomal protein L3 IVR12_00778 24 271 Phosphoglycerate kinase IVR12_01713 43 268 l lactate dehydrogenase IVR12_00437 34 266 Translation initiation factor IF2 IVR12_00451 77 260 30S ribosomal protein S5 IVR12_00761 18 253 Putative aminoacid ABC...”
lp_1033 ribosomal protein L3 from Lactobacillus plantarum WCFS1
56% identity, 94% coverage
- Oleuropein Transcriptionally Primes Lactobacillus plantarum to Interact With Plant Hosts
Santamaría, Frontiers in microbiology 2019 - “...2 ). Nine of these genes coding for the corresponding ribosomal proteins ( lp_0009 [RPLS6], lp_1033 [RPL3], lp_1034 [RPL4], lp_1035 [RPL23], lp_1036 [RPL2], lp_1038 [RPLS19], lp_1039 [RPL22], lp_1045 [RPL14], lp_1053 [RPS5]), were down-regulated ( Supplementary Table S2 ). In addition, genes required to counter stress that...”
- Identification of prebiotic fructooligosaccharide metabolism in Lactobacillus plantarum WCFS1 through microarrays
Saulnier, Applied and environmental microbiology 2007 - “...NS 1.2 1.1 Protein synthesis lp_0538 lp_0578 lp_1033 lp_1035 lp_1036 lp_1038 lp_1040 lp_1041 lp_1043 lp_1044 lp_1045 lp_1047 lp_1051 lp_1055 lp_1639...”
SERP1831 ribosomal protein L3 from Staphylococcus epidermidis RP62A
52% identity, 97% coverage
SE1824 50S ribosomal protein L3 from Staphylococcus epidermidis ATCC 12228
52% identity, 97% coverage
- Conserved genes in a path from commensalism to pathogenicity: comparative phylogenetic profiles of Staphylococcus epidermidis RP62A and ATCC12228
Wei, BMC genomics 2006 - “...extracellular functions, were also found in their surface proteome. This makes RpsL (SE0309) and RplC (SE1824), the two ribosomal proteins which have more non-synonymous substitutions than expected in our analysis more interesting. RpsL, protein S12 of the small subunit of the ribosome is known to control...”
- “...gamma-synthase 2 0 1.0000 0.0743 SE1828 SERP1836 DNA topoisomerase III topB 2 0 1.0000 0.0743 SE1824 SERP1831 50S ribosomal protein L3 2 0 1.0000 0.0759 SE0309 SERP0186 30S ribosomal protein S12 2 0 1.0000 0.0766 SE0463 SERP0349 putative deoxyribodipyrimidine photolyase 2 0 1.0000 0.0766 SE2067 SERP2080...”
Q1GBL8 Large ribosomal subunit protein uL3 from Lactobacillus delbrueckii subsp. bulgaricus (strain ATCC 11842 / DSM 20081 / BCRC 10696 / JCM 1002 / NBRC 13953 / NCIMB 11778 / NCTC 12712 / WDCM 00102 / Lb 14)
53% identity, 95% coverage
Sca_1735 50S ribosomal protein L3 from Staphylococcus carnosus subsp. carnosus TM300
52% identity, 97% coverage
LSEI_2503 Ribosomal protein L3 from Lactobacillus casei ATCC 334
56% identity, 94% coverage
P60449 Large ribosomal subunit protein uL3 from Staphylococcus aureus (strain N315)
Q6GEI3 Large ribosomal subunit protein uL3 from Staphylococcus aureus (strain MRSA252)
SA2047 50S ribosomal protein L3 from Staphylococcus aureus subsp. aureus N315
SAV2250 50S ribosomal protein L3 from Staphylococcus aureus subsp. aureus Mu50
SAOUHSC_02512 ribosomal protein L3, putative from Staphylococcus aureus subsp. aureus NCTC 8325
SACOL2239 50S ribosomal protein L3 from Staphylococcus aureus subsp. aureus COL
EKM74_RS05630, SA_RS11765 50S ribosomal protein L3 from Staphylococcus aureus
52% identity, 97% coverage
- Tiamulin-Resistant Mutants of the Thermophilic Bacterium Thermus thermophilus
Killeavy, Antibiotics (Basel, Switzerland) 2020 - “...radiodurans (Accession number Q9RXK2); Eco, Escherichia coli (Accession number P60438); Sau, Staphylococcus aureus (Accession number P60449); Bhy, Brachyspira hyodysenteriae (Accession number A0A2K9JGD3) ( B ) Interaction of ribosomal protein uL3 and 23S rRNA at the tiamulin binding site, based on the crystal structures of ribosomes from...”
- Identification of N-terminal protein processing sites by chemical labeling mass spectrometry
Misal, Rapid communications in mass spectrometry : RCM 2019 - “...25 M PKMKTHR G P66276 Ribosomal protein L35 Cytoplasm 5 5 26 M TKGILGR K P60449 Ribosomal protein L3 Cytoplasm 12 12 27 M TMTDPIADMLTR V P66630 Ribosomal protein S8 Cytoplasm 16 16 28 M AQVEYR G P66646 Ribosomal protein S9 Cytoplasm 5 5 29 M...”
- Structural and Functional Dynamics of Staphylococcus aureus Biofilms and Biofilm Matrix Proteins on Different Clinical Materials
Hiltunen, Microorganisms 2019 - “...Q931Q3 50S ribosomal protein L28 Q6GHL1 50S ribosomal protein L29 Q6GEJ1 50S ribosomal protein L3 Q6GEI3 50S ribosomal protein L30 Q6GEK1 50S ribosomal protein L31 Q6GEV5 50S ribosomal protein L35 Q6GG26 50S ribosomal protein L4 Q6GEI4 50S ribosomal protein L5 Q99S33 50S ribosomal protein L6 Q99S36...”
- Characterization of genetic changes associated with daptomycin nonsusceptibility in Staphylococcus aureus
Ma, PloS one 2018 - “...in the previous studies, including two nonsynonymous mutations within the 50S ribosomal L3 protein (gene SA2047) in both the JH4 and JH5 strains, two substitutions upstream of lysine decarboxylase gene (SA0439) in JH4, and a nonsynonomous substitution in the vraG gene of JH5. However, we did...”
- “...SNPs in DNS strains, including two nonsynonymous mutations within the 50S ribosomal L3 protein (gene SA2047) of both the JH4 and JH5 strains, two substitutions in the JH4 strain upstream of a lysine decarboxylase (SA0439) gene which potentially interacts with BlaR1; the integral membrane protein that...”
- Secretome analysis revealed adaptive and non-adaptive responses of the Staphylococcus carnosus femB mutant
Nega, Proteomics 2015 - “...homolog Sca_0720 SA0944 pdhB SACOL1103 10 35.2 4.6 RplC 50S ribosomal protein L3 homolog Sca_1735 SA2047 rplC SACOL_2239 2.2 + 23.7 9.6 RplE 50S ribosomal protein P5 homolog Sca_1723 SA2035 rplE SACOL2227 5.1 20.2 9.0 RplF Probable 50S ribosomal protein L6 Sca_1720 SA2033 rplF SACOL2224 3.5...”
- Transcriptional profiles of the response of methicillin-resistant Staphylococcus aureus to pentacyclic triterpenoids
Chung, PloS one 2013 - “...rpmB 50S ribosomal protein L28 6.3 Translation SA2039 rpmC 50S ribosomal protein L29 9.4 Translation SA2047 rplC 50S ribosomal protein L3 4.9 Translation SA2030 rpmD 50S ribosomal protein L30 6.2 Translation SA1922 rpmE 50S ribosomal protein L31 type B 4.8 Translation SAS033 rpmF 50S ribosomal protein...”
- Serine/threonine phosphatase Stp1 contributes to reduced susceptibility to vancomycin and virulence in Staphylococcus aureus
Cameron, The Journal of infectious diseases 2012 - “...permease ABC transporter, defense 633 SNP Ala580Val SA1702 SA2047 yvqF rplC Protein of the VraSR operon 50S ribosomal protein L3 Cell wall/outer membrane...”
- An RpoB mutation confers dual heteroresistance to daptomycin and vancomycin in Staphylococcus aureus
Cui, Antimicrobial agents and chemotherapy 2010 - “...C C A T T G T SA0500 SA1826 SA2042 SA2047 SA2047 rpoB RNA polymerase beta chain Hypothetical protein 50S ribosomal protein L22 50S ribosomal protein L3 (BL3)...”
- Direct targets of CodY in Staphylococcus aureus
Majerczyk, Journal of bacteriology 2010 - “...SA0012 ilvA1 SA2042 SA2043 ilvD ilvB SA2044 SA2045 SA2046 SA2047 SA2048 SA2049 SA2050 SA0600 ilvN ilvC leuA leuB leuC leuD ilvA ilvE Methionine SA0431 SA0430...”
- Characterizing the effects of inorganic acid and alkaline shock on the Staphylococcus aureus transcriptome and messenger RNA turnover
Anderson, FEMS immunology and medical microbiology 2010 - “...2.5 phnD SA0128 phosphonate ABC transporter Energy production and conversion sa_c4225s3576_a_at 10.8 ND 5 leuB SA2047 3-isopropylmalate dehydrogenase sa_c8930s7847_a_at 2.4 5 5 SA0763 oxidoreductase sa_c8671s7618_a_at 2.3 2.5 5 SA0959 NADH-dependent flavin oxidoreductase sa_c5174s4471_a_at 4.0 2.5 5 SA2321 oxidoreductase Coenzyme transport and metabolism sa_c3204s2753_a_at 4.8 ND 5...”
- Microarray analysis of toxicogenomic effects of ortho-phenylphenol in Staphylococcus aureus
Jang, BMC genomics 2008 - “...50S ribosomal protein L4; ribosomal protein L4 rpl D Translation, ribosomal structure and biogenesis sa_c4888s4195_a_at SA2047 0.00069 2.3 50S ribosomal protein L3; ribosomal protein L3 (BL3) rpl C Translation, ribosomal structure and biogenesis sa_c9963s8658_a_at SA2048 0.00245 2.4 30S ribosomal protein S10; ribosomal protein S10 (BS13) rps...”
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- The SAV1322 gene from Staphylococcus aureus: genomic and proteomic approaches to identification and characterization of gene function
Kim, BMC microbiology 2016 - “...Elongation factor Tu 123 Tuf SAV0548 Down A070 gi|15925240 50S ribosomal protein L3 516 rplC SAV2250 Down A076 gi|15924709 30S ribosomal protein S4 532 rpsD SAV1719 Down A096 gi|15924253 Prolyl-tRNA synthetase 176 proS SAV1263 Down A108 gi|15925214 DNA-directed RNA polymerase subunit alpha 905 rpoA SAV2224 Down...”
- Insights into the global effect on Staphylococcus aureus growth arrest by induction of the endoribonuclease MazF toxin
Sierra, Nucleic acids research 2020 - “...ribosome [GO:0003735] Tuf SAOUHSC_00530 Elongation factor Tu [591/UACUUA] [595/UACAUU] [743/UACAUG] [928/UACGUA] Translational elongation [GO:0006414] rplC SAOUHSC_02512 50S ribosomal protein L3 [324/UACUUU] Structural constituent of ribosome [GO:0003735] tadA SAOUHSC_00541 Hypothetical protein []8/UACAUA n/a trnaT SAOUHSC_T00055 tRNA-Thr 7/UACAUA[] n/a hemA SAOUHSC_01776 Glutamyl-tRNA reductase [455/CACAUA] Glutamyl-tRNA reductase activity [GO:0008883]...”
- The isolation of Staphylococcus aureus tea tree oil-reduced susceptibility mutants
Cuaron, Phytotherapy research : PTR 2014 - “...family transposase for IS1272 A 2264139 G 2264139 SAOUHSC_02448/SAOUHSC_02449 hydrolase 6-phospho-beta-galactosidase A 2272936 T 2272936 SAOUHSC_02512 ( rplC )/SAOUHSC_02515 50S ribosomal protein L3 putative membrane protein C 2318290 A 2318290 SAOUHSC_02638/SAOUHSC_A02505 membrane protein hypothetical protein A 2425210 G 2425210 SAOUHSC_02750/SAOUHSC_02751 ( pnbA ) APC family amino...”
- 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 - “...SACOL2226 SACOL2227 SACOL2228 SACOL2229 SAV2247 SACOL2234 SACOL2235 SACOL2238 SACOL2239 rpsL rpsG fusA rplQ rpoA rpmJ infA rplO rplF rpsH rpsN2 rplE rplX rplN...”
- Parallel evolution of linezolid-resistant Staphylococcus aureus in patients with cystic fibrosis
Pitcher, Microbiology spectrum 2023 - “...ribosome proteins/modifiers Isolate Linezolid MIC mutS, mutL SA_RS06425 SA_RS06430 23S rRNA G2576 a cfr rplC SA_RS11765 rlmI SA_RS05285 rluD SA_RS05915 rlmN SA_RS06020 rplD SA_RS11760 rpsC SA_RS11735 rpsJ SA_RS11770 rpsD SA_RS08675 HP20814.051 4 wt wt Absent wt wt wt wt wt wt wt wt AF4001 4 wt...”
- Transcriptomic Analysis Revealed Antimicrobial Mechanisms of Lactobacillus rhamnosus SCB0119 against Escherichia coli and Staphylococcus aureus
Peng, International journal of molecular sciences 2022 - “...ribosomal protein L23 EKM74_RS05625 145.16 12.67 3427.73 563.02 4.561522 rplD ; 50S ribosomal protein L4 EKM74_RS05630 188.98 15.87 7819.97 221.75 5.37082 rplC ; 50S ribosomal protein L3 EKM74_RS05635 294.61 86.56 9259.91 978.26 4.97412 rpsJ ; 30S ribosomal protein S10 EKM74_RS07510 151.39 9.3 705.28 120.89 2.219912 rplI...”
LBA0291 50S ribosomal protein L3 from Lactobacillus acidophilus NCFM
51% identity, 98% coverage
5li0E / Q2FW06 5li0E (see paper)
52% identity, 95% coverage
5nrgB / Q2FW06 The crystal structure of the large ribosomal subunit of staphylococcus aureus in complex with rb02 (see paper)
52% identity, 94% coverage
MMCAP2_0671 50S ribosomal protein L3 from Mycoplasma mycoides subsp. capri str. GM12
50% identity, 96% coverage
STH3075 50S ribosomal protein L3 from Symbiobacterium thermophilum IAM 14863
48% identity, 95% coverage
CD0073 50S ribosomal protein L3 from Clostridium difficile 630
CD630_00730 50S ribosomal protein L3 from Clostridioides difficile 630
52% identity, 94% coverage
- Semiquantitative analysis of clinical heat stress in Clostridium difficile strain 630 using a GeLC/MS workflow with emPAI quantitation
Ternan, PloS one 2014 - “...unit by itself, with a further four transcriptional units ( 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...”
- Different Resistance Mechanisms for Cadazolid and Linezolid in Clostridium difficile Found by Whole-Genome Sequencing Analysis
Caspers, Antimicrobial agents and chemotherapy 2017 (secret) - Complete genome sequence of the Clostridium difficile laboratory strain 630Δerm reveals differences from strain 630, including translocation of the mobile element CTn5
van, BMC genomics 2015 - “...Synonymous 84227 89522 substitution C>T CD630_00580 tuf1 Elongation factor EFTu/EF1A Synonymous 103225 108520 substitution G>T CD630_00730 rplC 50S ribosomal protein L3 Synonymous 610336 615631 substitution G>A CD630_05140 cwpV Cell surface protein Val>Ile 610480 615775 substitution C>T CD630_05140 cwpV Cell surface protein Synonymous 610563 610564 615859 615861...”
MBOVPG45_RS01305 50S ribosomal protein L3 from Mycoplasmopsis bovis PG45
47% identity, 78% coverage
7s9uD / P42920 44sr3c ribosomal particle (see paper)
47% identity, 94% coverage
FN1645 LSU ribosomal protein L3P from Fusobacterium nucleatum subsp. nucleatum ATCC 25586
50% identity, 95% coverage
- Proteomics of Fusobacterium nucleatum within a model developing oral microbial community
Hendrickson, MicrobiologyOpen 2014 - “...FN1628, FN1629, FN1630, FN1631, FN1632, FN1634, FN1635, FN1637, FN1638, FN1639, FN1640, FN1641, FN1642, FN1643, FN1644, FN1645, FN1646, FN1656, FN1657, FN1781, FN1828, FN1879, FN1979, FN2037, FN2038, FN2039, FN2040. 3 Covers FN0040, FN0054, FN0067, FN0069, FN0070, FN0110, FN0298, FN0299, FN0405, FN0466, FN0506, FN0611, FN0697, FN0753, FN0754, FN0755, FN1268,...”
MHJ_0190 50S ribosomal protein L3 from Mycoplasma hyopneumoniae J
47% identity, 91% coverage
SCO4702 50S ribosomal protein L3 from Streptomyces coelicolor A3(2)
44% identity, 94% coverage
- System-Wide Analysis of the GATC-Binding Nucleoid-Associated Protein Gbn and Its Impact on Streptomyces Development
Du, mSystems 2022 - “...promoter region. These genes include many genes from dcw cluster, 50S ribosomal protein gene cluster (SCO4702 to SCO4727), tRNAs (SCOt02 to SCOt50), atrA , redY , and gbn itself ( Table1 and Fig.3 ). Interestingly, Gbn not only bound strongly to the promoter regions of five...”
- “...N -acetylmuramoylalanyl- d -glutamyl-2,6-diaminopimelate- d -alanyl-alanyl ligase) 227 285 5 10 7.37 14.21 0.10 0.28 SCO4702 RplC (50S ribosomal protein L3) 459 511 34 37 12.19 22.16 0.12 0.27 SCO4707 RplV (50S ribosomal protein L22) 290 388 198 196 15.80 25.17 0.04 0.30 SCO4713 RplX (50S...”
- The Streptomyces coelicolor Small ORF trpM Stimulates Growth and Morphological Development and Exerts Opposite Effects on Actinorhodin and Calcium-Dependent Antibiotic Production
Vassallo, Frontiers in microbiology 2020 - “...S4 1.82 8.98 10 5 Translation SCO1599 50S ribosomal protein L35 1.59 3.90 10 3 SCO4702 50S ribosomal protein L3 1.47 1.65 10 2 SCO4702 50S ribosomal protein L3 1.30 3.66 10 2 SCO4702 50S ribosomal protein L3 2.53 3.36 10 6 SCO4703 50S ribosomal protein...”
- In Vivo Characterization of the Activation and Interaction of the VanR-VanS Two-Component Regulatory System Controlling Glycopeptide Antibiotic Resistance in Two Related Streptomyces Species
Novotna, Antimicrobial agents and chemotherapy 2015 - “...published primers, qvanH-F and qvanH-R (30), and gene SCO4702 as the internal normalization control (28). Primer pair qvanHst-F and qvanHst-R for qRT-PCR...”
- “...which has 94% nucleotide sequence identity to SCO4702, was used as the internal normalization control. qRT-PCR determinations were performed in triplicate...”
- Transcriptomic analysis of liquid non-sporulating Streptomyces coelicolor cultures demonstrates the existence of a complex differentiation comparable to that occurring in solid sporulating cultures
Yagüe, PloS one 2014 - “...Oxidoreductase 1.7 0.2 SCO4701 30S ribosomal protein S10 1.2 1.5 SCO1343 Uracil-DNA glycosylase 1.2 0.3 SCO4702 50S ribosomal protein L3 0.5 2 SCO1600 Translation initiation factor IF-3 1.2 0.9 SCO4703 50S ribosomal protein L4 0.4 2.1 SCO1631 Helicase 1.2 0.8 SCO4712 50S ribosomal protein L14 0.7...”
- 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 - “...SCO0527 SCO5371 SCO5477 SCO1598 SCO4703 SCO4653 SCO4649 SCO4702 SCO4721 SCO4718 SCO5595 SCO4091 SCO1480 SCO5077 SCO1947 SCO5624 SCO4711 SCO3906 SCO5625 SCO4809...”
- Quantitative proteomics analysis of Streptomyces coelicolor development demonstrates that onset of secondary metabolism coincides with hypha differentiation
Manteca, Molecular & cellular proteomics : MCP 2010 - “...SCO2620 SCO5221 SCO5625 SCO4710 SCO4719 SCO4721 SCO3909 SCO3970 SCO4713 SCO3874 SCO2562 SCO1600 SCO4702 SCO1491 6 7 6 6 6 8 8 6 6 6 6 6 6 7 7 7 2 3 2 32 32...”
- Comparative genomics of Streptomyces avermitilis, Streptomyces cattleya, Streptomyces maritimus and Kitasatospora aureofaciens using a Streptomyces coelicolor microarray system
Hsiao, Antonie van Leeuwenhoek 2008 - “...protein S7 0.57 0.23 0.68 0.12 SCO4701 30S ribosomal protein S10 1.19 1.17 1.16 0.21 SCO4702 50S ribosomal protein L3 0.92 0.02 0.84 0.49 SCO4703 50S ribosomal protein L4 1.16 0.91 0.59 0.23 SCO4704 50S ribosomal protein L23 0.85 1.44 1.24 0.36 SCO4705 50S ribosomal protein...”
- 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 - “...SCO3088, SCO3285, SCO3286, SCO5166, SCO6958; the TTA-containing gene SCO6638; and the ribosomal protein genes SCO4648, SCO4702, SCO4705, SCO4717. See Additional File 2 for these results. 3 from ScoDB [55] 4 from a Welch t-test applying the Benjamini and Hochberg multiple testing correction 5 average pfp (Probability...”
- “...selected differentially expressed genes (SCO6808, SCO7657, SCO4295, SCO5013, SCO3088, SCO3285, SCO3286, SCO5166, SCO6958, SCO6638, SCO4648, SCO4702, SCO4705, SCO4717) were designed using either Primer Express v.2 software (Applied Biosystems) or Primer 3 software [ 52 ]. Five g samples of each of the 16 RNA preparations from...”
C9YW78 Large ribosomal subunit protein uL3 from Streptomyces scabiei (strain 87.22)
45% identity, 94% coverage
BL1578 50S ribosomal protein L3 from Bifidobacterium longum NCC2705
45% identity, 94% coverage
9c4gd / A0A1G9KW65 Cutibacterium acnes 50s ribosomal subunit with clindamycin bound (see paper)
43% identity, 95% coverage
A4ST06 Large ribosomal subunit protein uL3 from Aeromonas salmonicida (strain A449)
ASA_4087 ribosomal protein L3 from Aeromonas salmonicida subsp. salmonicida A449
48% identity, 95% coverage
NGO1838 RplC from Neisseria gonorrhoeae FA 1090
NMB0142 50S ribosomal protein L3 from Neisseria meningitidis MC58
44% identity, 95% coverage
- Global Network Analysis of Neisseria gonorrhoeae Identifies Coordination between Pathways, Processes, and Regulators Expressed during Human Infection
McClure, mSystems 2020 - “...a number of ribosomal protein genes, NGO1834 ( rpsS ), NGO1835 ( rplB ), and NGO1838 ( rplC ), and several hypothetical proteins. These hypothetical proteins include NGO0672, NGO1301, NGO1861, NGO2068 (a putative membrane protein), NGO1518, NGO0791 (containing a domain with lipoic acid-binding regulatory protein homology),...”
- Proteomic analysis of Neisseria gonorrhoeae biofilms shows shift to anaerobic respiration and changes in nutrient transport and outermembrane proteins
Phillips, PloS one 2012 - “...subunit beta tRNA aminoacylation 1.434 (1) NGO1843 FusA; elongation factor G Translation factors 1.381 (1) NGO1838 RplC; 50S ribosomal protein L3 Ribosomal proteins: synthesis and modification 1.297 (2) NGO2024 RplM; 50S ribosomal protein L13 Ribosomal proteins: synthesis and modification 1.123 (1) Transport and binding proteins NGO2093...”
- Manganese regulation of virulence factors and oxidative stress resistance in Neisseria gonorrhoeae
Wu, Journal of proteomics 2010 - “...30S ribosomal protein S5 rpsE B 18231 NGO2025 30S ribosomal protein S9 rpsI B 14363 NGO1838 50S ribosomal protein L3 rpIC B 22663 NGO1837 50S ribosomal protein L4 rpID B 23288 NGO0584 50S ribosomal protein L9 rpII B 15687 NGO1853 50S ribosomal protein L10 rpIJ B...”
- Molecular characterization and identification of proteins regulated by Hfq in Neisseria meningitidis
Pannekoek, FEMS microbiology letters 2009 - “...NMB0138 FusA W + Elongation factor G Protein translation and modification 77 244 4.8184 4a NMB0142 RplC W + 50S ribosomal protein L3 Ribosomal protein synthesis and modification 22 678 10.7606 4a NMB0154 RplE W 50S ribosomal protein L5 Ribosomal protein synthesis and modification 20 322...”
8rd8Af / A0A0M4T1M3 8rd8Af (see paper)
46% identity, 95% coverage
sll1799 50S ribosomal protein L3 from Synechocystis sp. PCC 6803
47% identity, 89% coverage
- Regulation of RNase E during the UV stress response in the cyanobacterium Synechocystis sp. PCC 6803
Watanabe, mLife 2023 - “...46 . In addition, the sRNA ncl0380 , which corresponds to the 5 UTR of sll1799 encoding ribosomal protein L3, was upregulated at both 1 and 2h after UV treatment, while the downstreamlocated ribosomal gene cluster was strongly downregulated at 1h after UV treatment and then...”
- Systematic and functional identification of small non-coding RNAs associated with exogenous biofuel stress in cyanobacterium Synechocystis sp. PCC 6803
Pei, Biotechnology for biofuels 2017 - “...Hypothetical protein 44 sll0048 Hypothetical protein 179 Nc110 (SyR5) 1.19 2.171 nc26 842,648842,758 <<> 40.5 sll1799 50S ribosomal protein L3 35 slr1894 Hypothetical protein 347 Nc26 1.201 0.635 nc41 1,190,7361,190,822 <>> 22.2 sll1783 Hypothetical protein 353 slr1852 Hypothetical protein 45 Nc41 (Ncr0480) 0.678 1.053 nc70 1,886,8951,887,070...”
- Strain of Synechocystis PCC 6803 with Aberrant Assembly of Photosystem II Contains Tandem Duplication of a Large Chromosomal Region
Tichý, Frontiers in plant science 2016 - “...product GT-P 488230 SNP TG F255C slr1609 fadD long-fatty-acid CoA ligase 842060 SNP CT R186Q sll1799 rpl3 50S ribosomal protein L3 GT-W 488268 SNP GA V268I slr1609 fadD long-fatty-acid CoA ligase 842060 SNP GT R186Q sll1799 rpl3 50S ribosomal protein L3 2354038 Del 5326 bp del...”
- Identification of substrain-specific mutations by massively parallel whole-genome resequencing of Synechocystis sp. PCC 6803
Kanesaki, DNA research : an international journal for rapid publication of reports on genes and genomes 2012 - “...GT-I strain-specific 842060 SNP C C C T C C 255 255 MAQ BWA mummer sll1799 rplC R185Q GT-I strain-specific 909360 SNP C C C T C C 255 255 MAQ BWA mummer sll1968 pmgA E93K GT-I strain-specific 1392586 SNP T T T C T T...”
- Gene expression patterns of sulfur starvation in Synechocystis sp. PCC 6803
Zhang, BMC genomics 2008 - “...Translation (sll1820( truA ), sll1099( tufA ), Ribosomal proteins (sll0767( rpl20 ), sll1745( rpl10 ), sll1799( rpl3 ), sll1801( rpl23 ), sll1802( rpl2 ), sll1803( rpl22 ), sll1804( rpl3 ), sll1805( rpl16 ), sll1806( rpl14 ), sll1812( rps5 ), sll1817( rps11 ), sll1819( rpl17 ), sll1821(...”
- “...of these significantly repressed ribosomal protein subunits genes are clustered on the Synechocystis chromosome (from sll1799 to sll1822 ). The transcription of the principle sigma factor SigA, encoded by rpoD ( sll0306 , cluster 7), was significantly induced at 24-hr time-point, and the ECF-type (group 3)...”
- DNA microarray analysis of redox-responsive genes in the genome of the cyanobacterium Synechocystis sp. strain PCC 6803
Hihara, Journal of bacteriology 2003 - “...linker protein sll1580, cpcC, phycocyanin-associated linker protein sll1799, rpl3, 50S ribosomal protein L3 sll1800, rpl4, 50S ribosomal protein L4 sll1801,...”
- Comparative analysis of chloroplast genomes: functional annotation, genome-based phylogeny, and deduced evolutionary patterns
De, Genome research 2002 - “...psbY 0.1192 slr0012 rbcS 0.1192 sll1744 rpl1 0.1192 sll1799 rpl3 0.1192 sll1810 rpl6 0.1192 sll1743 rpl11 0.1192 sll1811 rpl18 0.1192 sll1812 rps5 0.1192...”
7unrD / Q9HWD5 7unrD
PA14_08850 50S ribosomal protein L3 from Pseudomonas aeruginosa UCBPP-PA14
Q9HWD5 Large ribosomal subunit protein uL3 from Pseudomonas aeruginosa (strain ATCC 15692 / DSM 22644 / CIP 104116 / JCM 14847 / LMG 12228 / 1C / PRS 101 / PAO1)
PA4263 50S ribosomal protein L3 from Pseudomonas aeruginosa PAO1
44% identity, 95% coverage
- Ligand: rna (7unrD)
- Gene Expression Profiling of Pseudomonas aeruginosa Upon Exposure to Colistin and Tobramycin
Cianciulli, Frontiers in microbiology 2021 - “...protein DppF 21.5 4.19 Transcription and translation tufB PA14_08680 Elongation factor Tu 92.01 3.09 rplC PA14_08850 50S ribosomal protein L3 27.97 ND rplD PA14_08860 50S ribosomal protein L4 23.35 2.05 tyrS PA14_10420 Tyrosyl-tRNA synthetase 37.72 11.48 orf2 PA14_12350 (dimethylallyl)adenosine tRNA methylthiotransferase 23.15 2.17 rimM PA14_15980 16S...”
- Proteome-wide identification of druggable targets and inhibitors for multidrug-resistant <i>Pseudomonas aeruginosa</i> using an integrative subtractive proteomics and virtual screening approach
Vemula, Heliyon 2025 - “...4723 Q9I5E0 396 O68822 1478 Q9HWD4 2560 Q9HU84 3642 Q9HZQ5 4724 Q9I5E1 397 O69077 1479 Q9HWD5 2561 Q9HU87 3643 Q9HZQ6 4725 Q9I5E5 398 O69754 1480 Q9HWD7 2562 Q9HU89 3644 Q9HZQ7 4726 Q9I5E7 399 O82852 1481 Q9HWD8 2563 Q9HU90 3645 Q9HZQ9 4727 Q9I5E8 400 O86422 1482 Q9HWD9...”
- Virtual Screening and Meta-Analysis Approach Identifies Factors for Inversion Stimulation (Fis) and Other Genes Responsible for Biofilm Production in Pseudomonas aeruginosa: A Corneal Pathogen
Emeka, Current issues in molecular biology 2024 - “...IF-2 1.45 0.0020 PA0904 lysC aspartate kinase alpha and beta chain 1.42 8.08 10 5 PA4263 rplC 50S ribosomal protein L3 1.30 0.0004 PA4742 truB tRNA pseudouridine 55 synthase 1.27 0.0006 cimb-46-00770-t004_Table 4 Table 4 List of top 25 down-regulated genes in biofilm. Locus Tag Gene...”
- <i>Pseudomonas aeruginosa</i> transcriptome analysis of metal restriction in <i>ex vivo</i> cystic fibrosis sputum
Neff, Microbiology spectrum 2024 - “...categories were consolidated (12 genes were included in both categoriesPA2402, PA3126, PA2424, PA2399, PA5556, PA2400, PA4263, PA4568, PA4432, PA4470, PA4741, PA4262and there were 35 unique key genes in total presented in Table 2 ). The list of key genes presented in Table 2 excludes basic maintenance...”
- Reorganization of gene network for degradation of polycyclic aromatic hydrocarbons (PAHs) in Pseudomonas aeruginosa PAO1 under several conditions
Yan, Journal of applied genetics 2017 - “...panel B), including 38 genes having functions of translation, ribosomal structure, and biogenesis. Among them, PA4263 is a heat shock protein involved in stress response, and PA4266 is an elongation factor whose activity reflects a cellular protective response (Nde et al. 2008 ). Fig. 4 Genes...”
- 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 - “...PA4252 PA4254 PA4257 PA4258 PA4259 PA4260 PA4261 PA4262 PA4263 PA4266 PA4267 PA4268 PA4271 PA4272 PA4274 PA4296 PA4306 PA4351 PA4352 PA4386 PA4425 PA4430 PA4431...”
- Toxicogenomic response of Pseudomonas aeruginosa to ortho-phenylphenol
Nde, BMC genomics 2008 - “...PA5561_atpI_at PA5561 2.558 0.0015 2.542 0.0015 ATP synthase protein I atp I Energy metabolism PA3818_at PA4263 2.746 0.00537 5.447 0.00537 extragenic suppressor protein SuhB Suh B Adaptation, protection PA4743_rbfA_at PA4743 2.824 0.0177 4.063 0.0177 ribosome-binding factor A rbf A Adaptation, protection PA5117_typA_at PA5117 3.136 0.000343 5.723...”
- “...upregulation of the cold shock protein: PA4743 ( rbf A) and the heat shock protein: PA4263 ( suh B) which are involved in stress response supports this hypothesis. The observed upregulation of translation may also indicate an increase in the synthesis of virulence factors, which can...”
- Proteomic, microarray, and signature-tagged mutagenesis analyses of anaerobic Pseudomonas aeruginosa at pH 6.5, likely representing chronic, late-stage cystic fibrosis airway conditions
Platt, Journal of bacteriology 2008 - “...intensity changea PA5427 PA5171 PA1155 PA1339 PA0588 PA4385 PA4263 PA3874 PA0519 PA0519 PA0519 PA1155 PA2097 PA1156 PA3392 PA4246 PA1800 PA4265 PA2639 PA3482...”
- “...(moaB1) PA3944 PA4236 (katA) PA4238 (rpoA) PA4246 (rpsE) PA4263 (rplC) PA4265 (tufA) PA4266 (fusA1) PA4273 (rplA) PA4385 (groEL) PA4403 (secA) PA4481 (mreB)...”
- Quorum-sensing antagonistic activities of azithromycin in Pseudomonas aeruginosa PAO1: a global approach
Nalca, Antimicrobial agents and chemotherapy 2006 - “...PA3841b PA3842 PA3976 PA3988 PA4004 PA4006 PA4059 PA4114 PA4235 PA4263 PA4441 PA4460 PA4495 PA4525 PA4567 PA4568 exoT hcpC pilH fda trpG trpD trpC pqsA cysP...”
- Microarray analysis and functional characterization of the nitrosative stress response in nonmucoid and mucoid Pseudomonas aeruginosa
Firoved, Journal of bacteriology 2004 - “...PA4226 PA4225 PA4266 PA5129 PA5128 PA4248 PA5054 PA4263 PA0963 PA4260 PA4762 PA4246 PA4385 PA4258 PA0447 Gene expression ratio (with GSNO stress/control)a...”
A0T0H8 Large ribosomal subunit protein uL3c from Phaeodactylum tricornutum (strain CCAP 1055/1)
43% identity, 94% coverage
7a0rB / Q9RXK2 50s deinococcus radiodurans ribosome bounded with mycinamicin i (see paper)
45% identity, 94% coverage
VF_0235 50S ribosomal protein L3 from Aliivibrio fischeri ES114
VF_0235 50S ribosomal subunit protein L3 from Vibrio fischeri ES114
47% identity, 94% coverage
BPSL3213 50S ribosomal protein L3 from Burkholderia pseudomallei K96243
43% identity, 95% coverage
- Unraveling the role of toxin-antitoxin systems in Burkholderia pseudomallei: exploring bacterial pathogenesis and interactions within the HigBA families
Chapartegui-González, Microbiology spectrum 2024 - “...). However, the mutants shared some relevant commonly repressed genes that were overexpressed in WT: BPSL3213, which encodes for a ribosomal protein ( rplC ); BPSL3426, two-component regulator; and the type II toxins BPSS0390 ( hicA ), BPSS1060 ( higB ), and BPSL0175 ( higB )....”
- “...BPSL0117), as well as genes that encode for ribosomal-related proteins (BPSL2159, BPSL2515, BPSL3318, BPSL3209, BPSL3210, BPSL3213, BPSL3204, BPSL3212, BPSL3211, and BPSL1508) were found. As it is shown in Table S1, some genes are differentially expressed under different conditions, and some are present in nearly all conditions....”
A0QSD1 Large ribosomal subunit protein uL3 from Mycolicibacterium smegmatis (strain ATCC 700084 / mc(2)155)
MSMEG_1436 ribosomal protein L3 from Mycobacterium smegmatis str. MC2 155
MSMEG_1436, MSMEI_1400 50S ribosomal protein L3 from Mycolicibacterium smegmatis MC2 155
41% identity, 96% coverage
- Interactome Analysis Identifies MSMEI_3879 as a Substrate of Mycolicibacterium smegmatis ClpC1
Ogbonna, Microbiology spectrum 2023 - “...0.02 0.01 A0QSL6 rpsK , MSMEG_1522, MSMEI_1486 30S ribosomal protein S11 0.03 0.03 0.07 0.07 A0QSD1 rplC , MSMEG_1436, MSMEI_1400 50S ribosomal protein L3 0.1 0.14 0.25 0.09 A0R3I9 rpmF , MSMEG_5489, MSMEI_5337 50S ribosomal protein L32 0.03 0.03 0.15 0.02 A0QSL5 rpsM , MSMEG_1521, MSMEI_1485...”
- Associating H2O2-and NO-related changes in the proteome of Mycobacterium smegmatis with enhanced survival in macrophage.
Ganief, Emerging microbes & infections 2018 - “...subunit beta) (EC 2.7.7.6) (RNA polymerase subunit beta) (transcriptase subunit beta) 2.7.7.6 0.39 Protein expression A0QSD1 rplC 50S ribosomal protein L3 N/A 0.25 Protein expression A0QSG4 rplF 50S ribosomal protein L6 N/A 0.25 Protein expression A0QS62 rplJ 50S ribosomal protein L10 N/A 0.25 Protein expression A0QSG8...”
- Interactome Analysis Identifies MSMEI_3879 as a Substrate of Mycolicibacterium smegmatis ClpC1
Ogbonna, Microbiology spectrum 2023 - “...rpsK , MSMEG_1522, MSMEI_1486 30S ribosomal protein S11 0.03 0.03 0.07 0.07 A0QSD1 rplC , MSMEG_1436, MSMEI_1400 50S ribosomal protein L3 0.1 0.14 0.25 0.09 A0R3I9 rpmF , MSMEG_5489, MSMEI_5337 50S ribosomal protein L32 0.03 0.03 0.15 0.02 A0QSL5 rpsM , MSMEG_1521, MSMEI_1485 30S ribosomal protein...”
- Monitoring global protein thiol-oxidation and protein S-mycothiolation in Mycobacterium smegmatis under hypochlorite stress
Hillion, Scientific reports 2017 - “...(+484)ATSVR(T) 11,57 (K)AASSGATVLC 80 (+484)VSK(D) 9,09 (R)FC 93 (+484)GAEGIENVTTASAFR(S) 6,91 Protein biosynthesis and quality control MSMEG_1436 RplC 50S ribosomal protein L3 (R)RPGSIGGC 154 (+484)ATPGR(V) 7,32 MSMEG_1521 RpsM 30S ribosomal protein S13 (R)KIEIGC 86 (+484)YQGLR(H) 21,77 MSMEG_6895 RpsR2 30S ribosomal protein S18 (R)VTGNC 57 (+484)VQHQR(D) 10,66 MSMEG_0839...”
- Gene Expression, Bacteria Viability and Survivability Following Spray Drying of Mycobacterium smegmatis
Lauten, Materials (Basel, Switzerland) 2010 - “...L1 rplA 1.4 11.8 0.001 88% MSMEG_1439 ribosomal protein L2 rplB 1.3 12.6 0.001 81% MSMEG_1436 ribosomal protein L3 rplC 1.2 11.4 0.001 97% MSMEG_1437 ribosomal protein L4/L1 family protein rplD 1.3 12.1 0.000 99% MSMEG_1467 ribosomal protein L5 1.8 11.8 0.000 100% MSMEG_1470 ribosomal protein...”
- Interactome Analysis Identifies MSMEI_3879 as a Substrate of Mycolicibacterium smegmatis ClpC1
Ogbonna, Microbiology spectrum 2023 - “..., MSMEG_1522, MSMEI_1486 30S ribosomal protein S11 0.03 0.03 0.07 0.07 A0QSD1 rplC , MSMEG_1436, MSMEI_1400 50S ribosomal protein L3 0.1 0.14 0.25 0.09 A0R3I9 rpmF , MSMEG_5489, MSMEI_5337 50S ribosomal protein L32 0.03 0.03 0.15 0.02 A0QSL5 rpsM , MSMEG_1521, MSMEI_1485 30S ribosomal protein S13...”
X0QHH3 Large ribosomal subunit protein uL3 from Rhodococcus wratislaviensis NBRC 100605
43% identity, 94% coverage
6dziD / A0QSD1 6dziD (see paper)
41% identity, 95% coverage
VC2596 ribosomal protein L3 from Vibrio cholerae O1 biovar eltor str. N16961
47% identity, 94% coverage
bglu_1g02580 Ribosomal protein L3 from Burkholderia glumae BGR1
44% identity, 95% coverage
DIP0473 50S ribosomal protein L3 from Corynebacterium diphtheriae NCTC 13129
43% identity, 94% coverage
NCgl0487 50S ribosomal protein L3 from Corynebacterium glutamicum ATCC 13032
cg0594 50S ribosomal protein L3 from Corynebacterium glutamicum ATCC 13032
43% identity, 94% coverage
- Transcriptome analysis of Corynebacterium glutamicum in the process of recombinant protein expression in bioreactors
Sun, PloS one 2017 - “...in transcription 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,...”
- “...were hypothetical proteins. Eleven genes encoded ribosomal proteins (NCgl1304, NCgl0538, NCgl1901, NCgl2261, NCgl0518, NCgl0515, NCgl0495, NCgl0487, NCgl0833, NCgl1325, NCgl0488); however, most of them were down-regulated under C . glutamicum EGFP, indicating that the translation process was suppressed with EGFP expression. There were two genes (NCgl0303, NCgl1526)...”
- Quinone-dependent D-lactate dehydrogenase Dld (Cg1027) is essential for growth of Corynebacterium glutamicum on D-lactate
Kato, BMC microbiology 2010 - “...a Annotation a mRNA level b LB CgXII cg0045 ABC-type transporter, permease component 0,1 n.d. cg0594 ribosomal protein L3 1,3 0,2 cg0598 ribosomal protein L2 1,7 0,2 cg0652 ribosomal protein S13 0,9 0,2 cg0653 ribosomal protein S11 1,6 0,2 cg0769 ABC-type transporter, permease component 0,2 0,7...”
- 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 - “...rpsG 30S ribosomal protein S7 J cg0593 0.53 0.31 rpsJ 30S ribosomal protein S10 J cg0594 0.52 0.44 rplC 50S ribosomal protein L3 J cg0597 0.44 0.26 rplW 50S ribosomal protein L23 J cg0600 0.54 0.31 rplV 50S ribosomal protein L22 J cg0602 0.58 0.28 rplP...”
Mvan_1305 ribosomal protein L3 from Mycobacterium vanbaalenii PYR-1
40% identity, 96% coverage
- Comparative functional pan-genome analyses to build connections between genomic dynamics and phenotypic evolution in polycyclic aromatic hydrocarbon metabolism in the genus Mycobacterium
Kweon, BMC evolutionary biology 2015 - “...genes include (locus tags from M. vanbaalenii PYR-1); Mvan_0002, Mvan_1234, Mvan_1235, Mvan_1236, Mvan_1258, Mvan_1280, Mvan_1282, Mvan_1305, Mvan_1308, Mvan_1311, Mvan_1312, Mvan_1334, Mvan_1337, Mvan_1339, Mvan_1347, Mvan_1434, Mvan_1435, Mvan_1436, Mvan_1470, Mvan_1489, Mvan_2209, and Mvan_2651. Phylogenetic trees were constructed by the maximum likelihood method using PhyML [ 80 ] with...”
RplC / b3320 50S ribosomal subunit protein L3 from Escherichia coli K-12 substr. MG1655 (see 11 papers)
rplC / P60438 50S ribosomal subunit protein L3 from Escherichia coli (strain K12) (see 8 papers)
RL3_ECOLI / P60438 Large ribosomal subunit protein uL3; 50S ribosomal protein L3 from Escherichia coli (strain K12) (see 14 papers)
8a3ld / P60438 8a3ld (see paper)
rplC / RF|NP_417779 50S ribosomal protein L3 from Escherichia coli K12 (see 12 papers)
A7ZSK9 Large ribosomal subunit protein uL3 from Escherichia coli O139:H28 (strain E24377A / ETEC)
NP_417779 50S ribosomal subunit protein L3 from Escherichia coli str. K-12 substr. MG1655
Q0TCE1 Large ribosomal subunit protein uL3 from Escherichia coli O6:K15:H31 (strain 536 / UPEC)
Q1R602 Large ribosomal subunit protein uL3 from Escherichia coli (strain UTI89 / UPEC)
b3320 50S ribosomal protein L3 from Escherichia coli str. K-12 substr. MG1655
ECs4185 50S ribosomal subunit protein L3 from Escherichia coli O157:H7 str. Sakai
46% identity, 94% coverage
- function: One of two assembly initiator proteins, it binds directly near the 3'-end of the 23S rRNA, where it nucleates assembly of the 50S subunit.
subunit: Part of the 50S ribosomal subunit (PubMed:10094780, PubMed:12809609, PubMed:16272117, PubMed:24844575, PubMed:25310980, PubMed:27906160, PubMed:27906161, PubMed:27934701, PubMed:365579). Forms a cluster with proteins L14 and L19. In pull-down experiments interacts with CedA (PubMed:28818726). - Ligand: rna (8a3ld)
- Metabolomic and proteomic investigations of impacts of titanium dioxide nanoparticles on Escherichia coli
Planchon, PloS one 2017 - “...10.4 A7ZV11 Protein synthesis u 145 50S ribosomal protein L3 E . coli O139:H28 22.2 A7ZSK9 Protein synthesis u 146 Succinyl-CoA ligase [ADP-forming] subunit beta E . coli O139:H28 41.4 A7ZJA8 TCA cycle u 147 50S ribosomal protein L21 E . coli O139:H28 11.6 A7ZS83 Protein...”
- The primary structure of ribosomal protein L3 from Escherichia coli 70 S ribosomes.
Muranova, FEBS letters 1978 (PubMed)- GeneRIF: N-terminus verified by Edman degradation on complete protein
- CRP and IHF act as host regulators in Royal Jelly's antibacterial activity
Xia, Scientific reports 2024 - “...Ribosomal subunit protein L31 rpmE 0.25 1.87E07 P62399 Ribosomal subunit protein L5 rplE 0.25 4.15E08 P60438 Ribosomal subunit protein L3 rplC 0.29 4.88E09 P0A7M6 Ribosomal subunit protein L29 rpmC 0.3 1.35E05 P0A7L0 Ribosomal subunit protein L1 rplA 0.32 6.28E08 P0AG55 Ribosomal subunit protein L6 rplF 0.33...”
- The Thioredoxin Fold Protein (TFP2) from Extreme Acidophilic Leptospirillum sp. CF-1 Is a Chaperedoxin-like Protein That Prevents the Aggregation of Proteins under Oxidative Stress
Muñoz-Villagrán, International journal of molecular sciences 2024 - “...subunit protein L2 rplB 8.76 0.006 P0ADZ0 50S ribosomal subunit protein L23 rplW 6.85 0.021 P60438 50S ribosomal subunit protein L3 rplC 6.31 0.002 P0A6M8 elongation factor G fusA 6.81 0.024 P0A6U3 5-carboxymethylaminomethyluridine-tRNA synthase subunit MnmG mnmG 5.09 0.027 P0CE48 translation elongation factor Tu 2 tufB...”
- The Nucleic Acid Knowledgebase: a new portal for 3D structural information about nucleic acids.
Lawson, Nucleic acids research 2024 - “...Annotation Transferase NAKB PANTHER protein class DNA metabolism protein/PC00009 PANTHER ( 27 ) UniProt id P60438 PDB Ligand Nonpolymer id/name ATP/ADENOSINE-5-TRIPHOSPHATE PDB ( 23 ) Experiment Method (abbr) X-ray PDB Method (full) X-RAY DIFFRACTION PDB Crystal Space Group P 21 21 2 PDB Software PHENIX PDB...”
- Computational design and evaluation of mRNA- and protein-based conjugate vaccines for influenza A and SARS-CoV-2 viruses
Elalouf, Journal, genetic engineering & biotechnology 2023 - “...viruses. The sequence of the constructed vaccine started with a 50S ribosomal adjuvant protein (UniProtKB: P60438) [ 62 , 63 ] following the linkers and epitopes of sequences of NA and HA of IAV and S protein of SARS-CoV-2 and ended with MITD (MHC I-targeting domain)...”
- Liquid-Liquid Phase Separation and Protective Protein Aggregates in Bacteria
Kuczyńska-Wiśnik, Molecules (Basel, Switzerland) 2023 - “...TnaA 0.89 830 0.538 0.141 0.005 19 P0ABT2 Dps 0.89 7698 0.527 0.126 0.012 20 P60438 50S ribosomal protein L3 0.88 5500 1.392 0.235 0.103...”
- A Continuous Assay Set to Screen and Characterize Novel Protein N-Acetyltransferases Unveils Rice General Control Non-repressible 5-Related N-Acetyltransferase2 Activity
Asensio, Frontiers in plant science 2022 - “...M AKEDNIEMQG 1.00.1 63.41.7 P0A7X3 RS9 30S ribosomal protein S9 1 - MAENQYYGTG 0.20.0 52.56.4 P60438 RL3 50S ribosomal protein L3 2 M IGLVGKKVGM 0.60.1 52.59.7 P22255 CYSQ 3(2),5-bisphosphate nucleotidase CysQ (EC 3.1.3.7) 1 - MLDQVCQLAR 1.2 52.4 P0AGJ5 YFIF Uncharacterized tRNA/rRNA methyltransferase YfiF (EC 2.1.1.-)...”
- FLASHIda enables intelligent data acquisition for top-down proteomics to boost proteoform identification counts
Jeong, Nature communications 2022 - “...top four selected proteins (two ribosomal proteins and two binding proteins; UniProtKB: P0ACF8, P0A7N1, P76344, P60438) with the four highest proteoform ID diversity. It also provides the manual validation results and possible interpretations for the modifications (see also Supplementary Figs. 23 27 for example annotations). In...”
- Tiamulin-Resistant Mutants of the Thermophilic Bacterium Thermus thermophilus
Killeavy, Antibiotics (Basel, Switzerland) 2020 - “...thermophilus (Accession number Q72I04); Dra, Deinococcus radiodurans (Accession number Q9RXK2); Eco, Escherichia coli (Accession number P60438); Sau, Staphylococcus aureus (Accession number P60449); Bhy, Brachyspira hyodysenteriae (Accession number A0A2K9JGD3) ( B ) Interaction of ribosomal protein uL3 and 23S rRNA at the tiamulin binding site, based on...”
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- Identification of Functional Interactome of Colistin Resistance Protein MCR-1 in Escherichia coli
Li, Frontiers in microbiology 2020 - “...P64596 Uncharacterized protein YraP 20,073 yraP 32 Q0TCG0 50S ribosomal protein L15 14,957 rplO 33 Q0TCE1 50S ribosomal protein L3 22,230 rplC 34 P0A7M6 50S ribosomal protein L29 7,269 rpmC 35 P0A7J3 50S ribosomal protein L10 17,757 rplJ 36 P0AG59 30S ribosomal protein S14 11,630 rpsN...”
- Peptidylarginine Deiminase Inhibitors Reduce Bacterial Membrane Vesicle Release and Sensitize Bacteria to Antibiotic Treatment
Kosgodage, Frontiers in cellular and infection microbiology 2019 - “...B7MSJ0 RNA-binding protein Hfq hfq 256917 132.47 Q1R638 50S ribosomal protein L17 rplQ 126430 128.85 Q1R602 50S ribosomal protein L3 rplC 69461 254.77 Q1R619 50S ribosomal protein L24 rplX 6484.4 75.48 B7N255 Protein-export protein SecB secB 136512 77.044 P14407 Fumarate hydratase class I, anaerobic fumB 15233...”
- Whole-genome sequencing analysis of two heat-evolved Escherichia coli strains
McGuire, BMC genomics 2023 - “...b3189 UDP-N-acetylglucosamine 1-carboxyvinyltransferase T10M 0.4 rpsH b3306 30S ribosomal subunit protein S8 R13C -0.5 rplC b3320 50S ribosomal subunit protein L3 V189I 0.1 rho b3783 transcription termination factor Rho T96I 0.6 rpoC b3988 RNA polymerase subunit beta' A595V, T1135I 0.6 dnaB b4052 replicative DNA helicase P264S...”
- CentiServer: A Comprehensive Resource, Web-Based Application and R Package for Centrality Analysis
Jalili, PloS one 2015 - “...rpsC (b3314), htpG (b0473), tufB (b3980), tufA (b3339), fusA (b3340), rpsG (b3341), rpsI (b3230), rplC (b3320), rplM (b3231), rplQ (b3294), rpoC (b3988) and ybcV (b0558). Except rplA (b3984) and htpG (b0473), all of these genes were marked as essential ones previously. The result of this analysis...”
- Escherichia coli toxin/antitoxin pair MqsR/MqsA regulate toxin CspD
Kim, Environmental microbiology 2010 - “...protein L23 rplD b3319 1.0 1.6 2.0 50S ribosomal subunit protein L4, erythromycin sensitivity rplC b3320 1.2 1.6 2.1 50S ribosomal subunit protein L3 rpsG b3341 1.1 1.9 2.0 30S ribosomal subunit protein S7 Cell wall/membrane and motility/chemotaxis csgG b1037 2.1 2.1 1.1 Curli production assembly/transport...”
- Analysis of promoter targets for Escherichia coli transcription elongation factor GreA in vivo and in vitro
Stepanova, Journal of bacteriology 2007 - “...rplD rplC rpsJ b3311 b3312 b3313 b3314 b3315 b3316 b3317 b3318 b3319 b3320 b3321 4.2 3.1 3.5 3.2 3.3 3.1 3.1 2.9 3.0 2.3 2.9 30S 50S 50S 30S 50S 30S 50S 50S 50S...”
- Global gene expression profiling of the asymptomatic bacteriuria Escherichia coli strain 83972 in the human urinary tract
Roos, Infection and immunity 2006 - “...b3309 b3295 b1094 c2758 b3310 b3298 b3231 b2621 Z2747 b3320 b3123 b3341 b3299 b2779 b3782 b3983 b2579 b1677 b2153 b0114 b3986 b0169 c4310 b4457 b3301 b2415...”
- YdgG (TqsA) controls biofilm formation in Escherichia coli K-12 through autoinducer 2 transport
Herzberg, Journal of bacteriology 2006 - “...rpsC rpmB rpsB rpsF rplU rpsR rpmG rplK rplP rpmC b3320 b3317 b3318 b3321 b3316 b3319 b3315 b3314 b3637 b0169 b4200 b3186 b4202 b3636 b3983 b3313 b3312 8.6 8...”
- Interfering with different steps of protein synthesis explored by transcriptional profiling of Escherichia coli K-12
Sabina, Journal of bacteriology 2003 - “...rpsE csgC hdeB b3524 b2601 b1261 b1264 b1493 b3517 b3320 b1263 b2600 b1260 b1973 b1262 b3340 b1779 b3321 b3308 b3304 b3616 b3339 b2155 b3829 b3317 b3296 b2913...”
- “...b3316 b3985 b3313 b3314 b0719 b3317 b3315 b3318 b1158 b3319 b2667 b3320 b2185 b3312 b3321 b2607 9.7 8.3 6.9 6.3 5.8 5.7 5.6 5.4 5.4 5.2 5.1 5.1 5.1 4.8 4.8 4.7...”
- Microarray analysis of orthologous genes: conservation of the translational machinery across species at the sequence and expression level
Jiménez, Genome biology 2003 - “...L23 Ribosomal protein 12 b3319 Yes** COG0088 J4 50S ribosomal protein L4 Ribosomal protein 12 b3320 Yes** COG0087 J4 50S ribosomal protein L3 Ribosomal protein 12 b3321 Yes** COG0051 J3 30S ribosomal protein S10 Ribosomal protein 13 b3339 Yes** COG0050 J1 Protein chain elongation factor EF-Tu...”
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- Global transcriptional response of Escherichia coli O157:H7 to growth transitions in glucose minimal medium
Bergholz, BMC microbiology 2007 - “...rplW -5.75 1 ECs4684 mioC -2.10 1 ECs4184 rplD -6.50 1 ECs4686 asnA -3.68 1 ECs4185 rplC -4.69 1 ECs4708 ilvC -3.31 1 ECs4186 rpsJ -5.93 1 ECs4757 yigM -2.00 1 ECs4189 - 3.24 2 ECs4758 metR -3.26 1 ECs4191 fusA -3.27 1 ECs4760 - 3.29...”
A7MPI7 Large ribosomal subunit protein uL3 from Cronobacter sakazakii (strain ATCC BAA-894)
46% identity, 94% coverage
NP_215215 50S ribosomal protein L3 from Mycobacterium tuberculosis H37Rv
MT0728 50S ribosomal protein L3 from Mycobacterium tuberculosis CDC1551
Rv0701 50S ribosomal protein L3 from Mycobacterium tuberculosis H37Rv
39% identity, 96% coverage
- Mycobacterium tuberculosis Mutations Associated with Reduced Susceptibility to Linezolid.
Zhang, Antimicrobial agents and chemotherapy 2016 - GeneRIF: The mutants with reduced bacillary susceptibility to linezolid harbor rrl and rplC mutations in about equal proportions
- 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 - “...MT0741.1, MT2517, MT3052.2, MT2118, MT0114, MT0736, MT0728, MT0747, MT1337, MT2117.1, MT0663, MT4041.1, MT1680, MT3567.1, MT0729, MT0742, MT0744, MT0681,...”
- Immunogenicity of Mycobacterial Extracellular Vesicles Isolated From Host-Related Conditions Informs About Tuberculosis Disease Status
Schirmer, Frontiers in microbiology 2022 - “...Rv2904c RpIS 1 Rv0714 RpIN 1.21 Rv0714 RpIN 0.86 Rv0704 RpIB 0.85 Rv0716 RpIE 0.84 Rv0701 RpIC 0.85 Cell wall and cell processes 89 Rv3763 LpqH 1.71 44 Rv3763 LpqH 7.13 Rv3875 EsxA 0.89 Rv3875 EsxA 2.89 Rv2346c EsxO 0.61 Rv3616c EspA 2.64 Rv1793 EsxN 0.55...”
- The In Vivo Transcriptomic Blueprint of Mycobacterium tuberculosis in the Lung
Coppola, Frontiers in immunology 2021 - “...ranks in the interquartile range (Rv0667, Rv3794, Rv3795, Rv2447, Rv2163c, Rv0006, Rv3608, Rv3547, Rv2068c, Rv0706, Rv0701, Rv3793, and Rv2981c), with the exception of the target gene (Rv2763c) of the pro-drug Para-aminosalicylic acid (PAS) which had an expression rank in the lower quartile ( Figure4 ). Of...”
- Integrating informatics tools and portable sequencing technology for rapid detection of resistance to anti-tuberculous drugs
Phelan, Genome medicine 2019 - “...(0) Cycloserine Rv2780 ald 0 (0) 12 (10) Rv3423c alr 3 (3) 0 (0) Linezolid Rv0701 rplC 1 (1) 0 (0) rrl rrl 2 (1) 0 (0) Bedaquiline Rv0678 Rv0678 5 (0) 2 (1) Clofazimine Rv0678 Rv0678 5 (0) 2 (1) Delamanid Rv3261 fbiA 1 (0)...”
- Deciphering drug resistance in Mycobacterium tuberculosis using whole-genome sequencing: progress, promise, and challenges
Cohen, Genome medicine 2019 - “...21 , 22 ] Linezolid Rrl NA 23S rRNA Target modification [ 23 ] rplC Rv0701 50S ribosomal protein L3 Target modification [ 24 ] Group B Clofazimine pepQ Rv2535c Putative Xaa-Pro aminopeptidase Drug efflux [ 20 ] Rv0678 Rv0678 Transcriptional regulator of mmpL5 Drug efflux...”
- Identification of Mycobacterial Ribosomal Proteins as Targets for CD4+ T Cells That Enhance Protective Immunity in Tuberculosis
Kennedy, Infection and immunity 2018 - “...protein library screen (Rv0640, Rv0652, Rv0682, Rv0683, Rv0700, Rv0701, Rv0707, Rv0714, Rv2058c, and Rv2904) (Fig. 1 and additional data not shown) were...”
- Signatures of Selection at Drug Resistance Loci in Mycobacterium tuberculosis
Mortimer, mSystems 2018 - “...PZA 0.88 0.62 0.84 N N folC Rv2447c PAS 0.66 0.78 0.11 Y N rplC Rv0701 LZD 0.57 0.77 0.21 N N a The number of distinct entries in the TB Drug Resistance Mutation Database for each gene is reported in the TB Dream column. b...”
- Molecular Targets Related Drug Resistance Mechanisms in MDR-, XDR-, and TDR-Mycobacterium tuberculosis Strains
Hameed, Frontiers in cellular and infection microbiology 2018 - “...membrane. pepQ ( Rv2535c ) 1,119 372 38,758.9 Cytoplasmic peptidase PepQ Possibly hydrolyses peptides rplC (Rv0701) 654 217 23,090.5 Encodes the 50S ribosomal L3 protein Formation of peptidyltransferase center of the ribosome LIN/SZD : Both act by fixation of an early step in protein synthesis Activity...”
- The effect of growth rate on pyrazinamide activity in Mycobacterium tuberculosis - insights for early bactericidal activity?
Pullan, BMC infectious diseases 2016 - “...P60729 50S ribosomal protein L4 3.99 4.72 Rv0722 P66181 50S ribosomal protein L30 3.09 4.66 Rv0701 P60442 50S ribosomal protein L3 3.76 4.17 Rv0716 P62403 50S ribosomal protein L5 3.32 3.98 Rv0717 P0A5X2 30S ribosomal protein S14 type Z 3.48 3.79 Rv0682 P41196 30S ribosomal protein...”
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Rmet_3317 50S ribosomal protein L3 from Cupriavidus metallidurans CH34
42% identity, 95% coverage
7f0dD / A5U087 Cryo-em structure of mycobacterium tuberculosis 50s ribosome subunit bound with clarithromycin (see paper)
39% identity, 95% coverage
B7C60_RS03620 50S ribosomal protein L3 from Vibrio fujianensis
46% identity, 94% coverage
RL3_DEIRA / Q9RXK2 Large ribosomal subunit protein uL3; 50S ribosomal protein L3 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)
44% identity, 92% coverage
- function: One of the primary rRNA binding proteins, it binds directly near the 3'-end of the 23S rRNA, where it nucleates assembly of the 50S subunit.
subunit: Part of the 50S ribosomal subunit. Forms a cluster with proteins L14 and L19. Also contacts proteins L13 and L17. - Tiamulin-Resistant Mutants of the Thermophilic Bacterium Thermus thermophilus
Killeavy, Antibiotics (Basel, Switzerland) 2020 - “...uL3 have been found. Tth, Thermus thermophilus (Accession number Q72I04); Dra, Deinococcus radiodurans (Accession number Q9RXK2); Eco, Escherichia coli (Accession number P60438); Sau, Staphylococcus aureus (Accession number P60449); Bhy, Brachyspira hyodysenteriae (Accession number A0A2K9JGD3) ( B ) Interaction of ribosomal protein uL3 and 23S rRNA at...”
SPC_3509 50S ribosomal protein L3 from Salmonella enterica subsp. enterica serovar Paratyphi C strain RKS4594
P60446 Large ribosomal subunit protein uL3 from Salmonella typhimurium (strain LT2 / SGSC1412 / ATCC 700720)
STM3440 50S ribosomal subunit protein L3 from Salmonella typhimurium LT2
SEN3268 50S ribosomal subunit protein L3 from Salmonella enterica subsp. enterica serovar Enteritidis str. P125109
SC3374 50S ribosomal subunit protein L3 from Salmonella enterica subsp. enterica serovar Choleraesuis str. SC-B67
46% identity, 94% coverage
- Antibacterial Components and Modes of the Methanol-Phase Extract from Commelina communis Linn
Liu, Plants (Basel, Switzerland) 2023 - “...SPC_3506 ), 50S ribosomal protein L4 ( SPC_3508 ), and 50S ribosomal protein L3 ( SPC_3509 ), indicating that protein translation was significantly inhibited in S. enterica ATCC15611 after being treated with Fragment 1. Conversely, in nitrogen metabolism, four DEGs were significantly upregulated (3.204-fold to 29.218-fold)...”
- “...Metabolic Pathway Gene ID Fold Change Gene Description Ribosome SPC_3510 0.064 30S ribosomal protein S10 SPC_3509 0.071 50S ribosomal protein L3 SPC_3508 0.076 50S ribosomal protein L4 SPC_2784 0.095 50S ribosomal protein L19 SPC_3505 0.13 30S ribosomal protein S19 SPC_2787 0.135 30S ribosomal protein S16 SPC_3415...”
- N-dodecanoyl-homoserine lactone influences the levels of thiol and proteins related to oxidation-reduction process in Salmonella
de, PloS one 2018 - “...Translation -0.903 1.148 -8.794 2.134 9.181 1.039 ND ND ND ND 50S ribosomal protein L3 P60446 rplC Translation 9.334 2.324 ND ND ND ND ND ND ND ND 50S ribosomal protein L6 P66313 rplF Translation 0.593 1.957 -0.186 0.328 ND ND 7.572 0.841 -9.383 1.241 50S...”
- Global transcriptional analysis of dehydrated Salmonella enterica serovar Typhimurium
Gruzdev, Applied and environmental microbiology 2012 - “...rplB (STM3437) rplW (STM3438) rplD (STM3439) rplC (STM3440) rpsJ (STM3441) fusA (STM3446) rpsG (STM3447) rplK (STM4149) rplA (STM4150) rplJ (STM4151) miaA...”
- 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 - “...5.89 3.0 3.0 0.002 0.008 0.011 0.014 0.005 0.025 STM3728 STM3440 STM3437 STM3425 STM3414 STM3438 rpmB rplC rplB rplF rplQ rplW 50S 50S 50S 50S 50S 50S 5.92 2.1...”
- Global transcriptomic analysis of ethanol tolerance response in Salmonella Enteritidis
He, Current research in food science 2022 - “...L15 SEN3255 rpsN 3.96 30S ribosomal protein S14 SEN3933 rplK 2.87 50S ribosomal protein L11 SEN3268 rplC 2.95 50S ribosomal protein L3 SEN2217 rplY 2.95 50S ribosomal protein L25 SEN3251 rpsE 3.72 30S ribosomal protein S5 Cell motility SEN3059 aer 2.01 Aerotaxis receptor protein SEN3058 SEN3058...”
- Isolation and characterization of ilvA, ilvBN, and ilvD mutants of Caulobacter crescentus
Tarleton, Journal of bacteriology 1991 - “...i1vBNl03 rec-526 zzz::TnS SC3373 ilvBN105 rec-526 zzz::TnS SC3374 ilvBN106 rec-526 zzz::TnS SC3375 ilvBNI08 rec-526 zzz::TnS SC3376 ilvBN112 rec-526 zzz::TnS...”
Q88QN5 Large ribosomal subunit protein uL3 from Pseudomonas putida (strain ATCC 47054 / DSM 6125 / CFBP 8728 / NCIMB 11950 / KT2440)
43% identity, 95% coverage
PGN_1868 50S ribosomal protein L3 from Porphyromonas gingivalis ATCC 33277
PG1938 ribosomal protein L3 from Porphyromonas gingivalis W83
46% identity, 92% coverage
- Pathway analysis for intracellular Porphyromonas gingivalis using a strain ATCC 33277 specific database
Hendrickson, BMC microbiology 2009 - “...PGN_1088 PGN_1219 PGN_1651 PGN_1852 PGN_1573 PGN_1575 PGN_1853 PGN_1854 PGN_1588 PGN_1590 PGN_1855 PGN_1861 PGN_1832 PGN_1840 PGN_1863 PGN_1868 PGN_1842 PGN_1843 PGN_1872 PGN_1890 PGN_1849 PGN_1850 PGN_1891 PGN_1856 PGN_1857 PGN_1857 PGN_1858 PGN_1860 PGN_1862 PGN_1864 PGN_1865 PGN_1866 PGN_1867 PGN_1869 PGN_1871 Proteins are indicated as increased, decreased or unchanged in abundance for...”
- VimA-dependent modulation of the secretome in Porphyromonas gingivalis
Osbourne, Molecular oral microbiology 2012 - “...2 0 Outer membrane protein PG1901 Cell envelope 32 kDa 7 0 Conserved hypothetical protein PG1938 Unknown 61 kDa 7 0 Table 3 MS analysis of missing proteins in FLL92 extracellular fraction showing molecular characteristics of the proteins Identified Proteins (15) Lanl Accession number Putative Role/Function...”
- “...membrane protein PG1901 Cell envelope OM Yes Yes 32 kDa 7 0 Conserved hypothetical protein PG1938 Unknown IM Yes Yes 61 kDa 7 0 # The subcellular localization was performed using Psort prediction server. * The N terminal signal sequence detection was performed using the iPsort....”
CBU_0238 ribosomal protein L3 from Coxiella burnetii RSA 493
40% identity, 98% coverage
- Identification of essential genes in Coxiella burnetii
Metters, Microbial genomics 2023 - “...Leucyl-tRNA synthetase CBU_0081 COG0442 Prolyl-tRNA synthetase CBU_1188 COG0172 Seryl-tRNA synthetase CBU_0241 COG0090 Ribosomal protein L2 CBU_0238 COG0087 Ribosomal protein L3 CBU_0239 COG0088 Ribosomal protein L4 CBU_0253 COG0097 Ribosomal protein L6P/L9E CBU_1748 COG0102 Ribosomal protein L13 CBU_0244 COG0092 Ribosomal protein S3 CBU_0262 COG0522 Ribosomal protein S4 and...”
FP1339 50S ribosomal protein L3 from Flavobacterium psychrophilum JIP02/86
44% identity, 92% coverage
- Stress Tolerance-Related Genetic Traits of Fish Pathogen Flavobacterium psychrophilum in a Mature Biofilm
Levipan, Frontiers in microbiology 2018 - “...GO:0016740, GO:0019843, GO:0006412 3.72 FP1338 50S ribosomal protein L4 rplD GO:0005840, GO:0003735, GO:0019843, GO:0006412 3.12 FP1339 50S ribosomal protein L3 rplC GO:0005840, GO:0003735, GO:0019843, GO:0006412 2.83 FP1340 30S ribosomal protein S10 rpsJ GO:0005840, GO:0000049, GO:0003735, GO:0006412 2.97 FP1341 Elongation factor G (EF-G) fusA GO:0005737, GO:0003746, GO:0003924,...”
Alvin_2363 50S ribosomal protein L3 from Allochromatium vinosum DSM 180
41% identity, 97% coverage
plu4726 50S ribosomal protein L3 from Photorhabdus luminescens subsp. laumondii TTO1
44% identity, 94% coverage
- Genetic and proteomic characterization of rpoB mutations and their effect on nematicidal activity in Photorhabdus luminescens LN2
Qiu, PloS one 2012 - “...peptidyl transferase cente 11.04 14708.8 1 0.5 1.27 0.69 1.34 26 50S ribosomal protein L3, plu4726 P. luminescens TT01 rplC Binds directly near the 3 end of the 23S rRNA, where it nucleates assembly of the 50S subunit; essential for peptidyltransferase activity; mutations in this gene...”
- “...nematicidal-producing strains non nematicidal-producing strains W/W R16/W R2/W R31/W R33/W 26 50S ribosomal protein L3, plu4726 P. luminescens TT01 rplC Binds directly near the 3 end of the 23S rRNA, where it nucleates assembly of the 50S subunit; essential for peptidyltransferase activity; mutations in this gene...”
RL3_THET8 / Q5SHN8 Large ribosomal subunit protein uL3; 50S ribosomal protein L3 from Thermus thermophilus (strain ATCC 27634 / DSM 579 / HB8) (see paper)
5a9zAE / Q5SHN8 of Thermous thermophilus ribosome bound to BipA-GDPCP (see paper)
Q72I04 Large ribosomal subunit protein uL3 from Thermus thermophilus (strain ATCC BAA-163 / DSM 7039 / HB27)
43% identity, 94% coverage
- function: One of the primary rRNA binding proteins, it binds directly near the 3'-end of the 23S rRNA, where it nucleates assembly of the 50S subunit.
subunit: Part of the 50S ribosomal subunit. Forms a cluster with proteins L14 and L19 - Ligand: rna (5a9zAE)
- Tiamulin-Resistant Mutants of the Thermophilic Bacterium Thermus thermophilus
Killeavy, Antibiotics (Basel, Switzerland) 2020 - “...organisms for whom tiamulin-resistance mutations in uL3 have been found. Tth, Thermus thermophilus (Accession number Q72I04); Dra, Deinococcus radiodurans (Accession number Q9RXK2); Eco, Escherichia coli (Accession number P60438); Sau, Staphylococcus aureus (Accession number P60449); Bhy, Brachyspira hyodysenteriae (Accession number A0A2K9JGD3) ( B ) Interaction of ribosomal...”
Psyr_4548 Ribosomal protein L3 from Pseudomonas syringae pv. syringae B728a
41% identity, 95% coverage
MXAN_3370 ribosomal protein L3 from Myxococcus xanthus DK 1622
41% identity, 97% coverage
EAMY_3386 50S ribosomal protein L3 from Erwinia amylovora CFBP1430
44% identity, 94% coverage
YPO0210 50S ribosomal protein L3 from Yersinia pestis CO92
YPTB3698 50S ribosomal protein L3 from Yersinia pseudotuberculosis IP 32953
45% identity, 94% coverage
G372_RS0100970 50S ribosomal protein L3 from Thioalkalivibrio thiocyanoxidans ARh2
43% identity, 95% coverage
PMI3255 50S ribosomal protein L3 from Proteus mirabilis HI4320
43% identity, 94% coverage
7jilC / A0A1M5L9Q4 7jilC (see paper)
43% identity, 92% coverage
MAB_3820c 50S ribosomal protein L3 from Mycobacterium abscessus ATCC 19977
40% identity, 92% coverage
PMM1558 50S ribosomal protein L3 from Prochlorococcus marinus sp. MED4
41% identity, 93% coverage
XAUB_40430 50S ribosomal protein L3 from Xanthomonas citri pv. aurantifolii str. ICPB 11122
XAC0972 50S ribosomal protein L3 from Xanthomonas axonopodis pv. citri str. 306
41% identity, 94% coverage
BruAb1_1238 RplC, ribosomal protein L3 from Brucella abortus biovar 1 str. 9-941
BAB1_1255 Ribosomal protein L3 from Brucella melitensis biovar Abortus 2308
41% identity, 92% coverage
8fmwAE / P94267 8fmwAE (see paper)
41% identity, 94% coverage
PD0437 50S ribosomal protein L3 from Xylella fastidiosa Temecula1
40% identity, 95% coverage
MG_151 50S ribosomal protein L3 from Mycoplasma genitalium G37
41% identity, 82% coverage
- Transcriptional response of Mycoplasma genitalium to osmotic stress
Zhang, Microbiology (Reading, England) 2011 - “...differential expression by microarray and represented important physiological roles, were chosen to confirm microarray results. MG_151, which encodes a ribosomal protein exhibiting relatively stable expression under osmotic shock, was used as the endogenous control. The primers selected for these genes are listed in Table 1 ....”
- “...observed by microarray analysis. This discrepancy could be due to variations in the expression of MG_151 expression upon osmotic shock. DISCUSSION Bacteria respond to stressful environmental conditions by altering the expression of genes that enhance their survival. In the case of M. genitalium , a cell-wall-free...”
HI0777 ribosomal protein L3 (rpL3) from Haemophilus influenzae Rd KW20
43% identity, 94% coverage
C6AUZ7 Large ribosomal subunit protein uL3 from Rhizobium leguminosarum bv. trifolii (strain WSM1325)
40% identity, 97% coverage
LA_0739 50S ribosomal protein L3 from Leptospira interrogans serovar lai str. 56601
LIC12873 50S ribosomal protein L3 from Leptospira interrogans serovar Copenhageni str. Fiocruz L1-130
43% identity, 93% coverage
- Extracellular proteome analysis of Leptospira interrogans serovar Lai
Zeng, Omics : a journal of integrative biology 2013 - “...in its genome. LA_0416 LA_0492 LA_0505 LA_0563 LA_0739 LA_0862 LA_1404 LA_1499 LA_1676 LA_1762 LA_2413 LA_2637 LA_2823 LA_3091 LA_3240 LA_3242 LA_3276 LA_3340...”
- “...- acn COG1225O COG0443O - - COG1048C LA_0416 LA_0739 LA_0862 LA_1499 LA_1676 LA_1762 LA_2823 LA_3276 LA_3340 LA_3394 LA_3416 LA_3437 LA_3442 LA_3705 LA_4324...”
- Global proteome analysis of Leptospira interrogans
Eshghi, Journal of proteome research 2009 - “...Ribosomal protein L2 LIC12870 0.9621.149 0.7510.858 1.140 NS NS NS 1.140 50S Ribosomal protein L3 LIC12873 NS NS NS 0.8831.446 0.5610.821 1.151 1.151 Ribosomal protein S12 LIC10755 NS NS NS 0.9131.169 0.7020.802 1.178 1.178 50S Ribosomal protein L15 LIC12854 NS NS NS 0.871.573 0.4740.731 1.263 1.263...”
A1S_3080 50S ribosomal protein L3 from Acinetobacter baumannii ATCC 17978
39% identity, 95% coverage
- Insights Into Mechanisms of Biofilm Formation in Acinetobacter baumannii and Implications for Uropathogenesis
Colquhoun, Frontiers in cellular and infection microbiology 2020 - “...5.76, 1.87 AB5075_UW, ATCC 17978 Rumbo-Feal et al., 2013 ; Penesyan et al., 2019 rplC A1S_3080 50S ribosomal protein L3 5.06, 2.13 AB5075_UW, ATCC 17978 Rumbo-Feal et al., 2013 ; Penesyan et al., 2019 rplS A1S_3161 50S ribosomal protein L19 3.95, 2.57 AB5075_UW, ATCC 17978 Rumbo-Feal...”
- Whole transcriptome analysis of Acinetobacter baumannii assessed by RNA-sequencing reveals different mRNA expression profiles in biofilm compared to planktonic cells
Rumbo-Feal, PloS one 2013 - “...3.06 A1S_3077 50S ribosomal protein L2 1.75 1.77 A1S_3079 50S ribosomal protein L4 1.87 1.59 A1S_3080 50S ribosomal protein L3 2.13 1.29 A1S_3104 ATP-dependent RNA helicase 1.64 0.23 A1S_3108 coproporphyrinogen III oxidase 0.28 0.33 A1S_3113 hypothetical protein 0.90 0.04 A1S_3134 glutamate dehydrogenase 1.26 3.21 A1S_3161 50S...”
DVU1303 ribosomal protein L3 from Desulfovibrio vulgaris Hildenborough
41% identity, 92% coverage
SMc01309 PROBABLE 50S RIBOSOMAL PROTEIN L3 from Sinorhizobium meliloti 1021
39% identity, 94% coverage
SO0231 ribosomal protein L3 from Shewanella oneidensis MR-1
43% identity, 95% coverage
Q2A5H0 Large ribosomal subunit protein uL3 from Francisella tularensis subsp. holarctica (strain LVS)
FTH_0231 ribosomal protein L3 from Francisella tularensis subsp. holarctica OSU18
FTN_0239 50S ribosomal protein L3 from Francisella tularensis subsp. novicida U112
42% identity, 95% coverage
7m4vD / B7IA39 A. Baumannii ribosome-eravacycline complex: 50s (see paper)
38% identity, 95% coverage
8c8xD / P60438 Cryo-em captures early ribosome assembly in action (see paper)
42% identity, 94% coverage
LOC101762479 50S ribosomal protein L3, chloroplastic from Setaria italica
42% identity, 73% coverage
B6UF84 Large ribosomal subunit protein uL3c from Zea mays
42% identity, 73% coverage
TDE0767 ribosomal protein L3 from Treponema denticola ATCC 35405
39% identity, 94% coverage
Q9A8V3 Large ribosomal subunit protein uL3 from Caulobacter vibrioides (strain ATCC 19089 / CIP 103742 / CB 15)
39% identity, 82% coverage
LOC21403616 50S ribosomal protein L3-2, chloroplastic from Morus notabilis
41% identity, 67% coverage
RK3_SPIOL / P82191 Large ribosomal subunit protein uL3c; 50S ribosomal protein L3, chloroplastic from Spinacia oleracea (Spinach) (see 2 papers)
40% identity, 64% coverage
- function: Component of the chloroplast ribosome (chloro-ribosome), a dedicated translation machinery responsible for the synthesis of chloroplast genome-encoded proteins, including proteins of the transcription and translation machinery and components of the photosynthetic apparatus.
subunit: Component of the chloroplast large ribosomal subunit (LSU). Mature 70S chloroplast ribosomes of higher plants consist of a small (30S) and a large (50S) subunit. The 30S small subunit contains 1 molecule of ribosomal RNA (16S rRNA) and 24 different proteins. The 50S large subunit contains 3 rRNA molecules (23S, 5S and 4.5S rRNA) and 33 different proteins.
6eriAD / P82191 6eriAD (see paper)
40% identity, 88% coverage
CTL0790 LSU ribosomal protein L3P from Chlamydia trachomatis 434/Bu
B0B8A2 Large ribosomal subunit protein uL3 from Chlamydia trachomatis serovar L2 (strain ATCC VR-902B / DSM 19102 / 434/Bu)
38% identity, 93% coverage
CNE02690 ribosomal large subunit assembly and maintenance-related protein from Cryptococcus neoformans var. neoformans JEC21
39% identity, 71% coverage
7oodb / P75580 Mycoplasma pneumoniae 50s subunit of ribosomes in chloramphenicol- treated cells (see paper)
39% identity, 91% coverage
RL3_RHOPA / P60456 Large ribosomal subunit protein uL3; 50S ribosomal protein L3; RRP-L3 from Rhodopseudomonas palustris (strain ATCC BAA-98 / CGA009) (see paper)
41% identity, 88% coverage
- function: One of the primary rRNA binding proteins, it binds directly near the 3'-end of the 23S rRNA, where it nucleates assembly of the 50S subunit.
subunit: Part of the 50S ribosomal subunit. Forms a cluster with proteins L14 and L19.
MPN165 ribosomal protein L3 from Mycoplasma pneumoniae M129
39% identity, 73% coverage
- ProTInSeq: transposon insertion tracking by ultra-deep DNA sequencing to identify translated large and small ORFs
Miravet-Verde, Nature communications 2024 - “...in the fitness (F) gene mpn624 and at the C-terminal region in the E gene mpn165 (encoding for ribosomal proteins RmpB and RplC, respectively). Notably, another insertion was found in MPNs02 , which we previously showed encodes a SEP of 12 aa 10 , 29 ....”
- “...Essentiality category 469,307 MPNs02 1 Unannotated SEP NE 546,063 MPN447 1 Hmw1 (adhesion) NE 218,775 MPN165 1 Ribosomal protein L3 (rplC) E 751,237 MPN624 3 Ribosomal protein L28 (rmpB) F A sequencing approach to explore protein translation in bacteria We performed DNA deep-sequencing of 39 MPN...”
ZCP4_RS03820 50S ribosomal protein L3 from Zymomonas mobilis subsp. mobilis str. CP4 = NRRL B-14023
40% identity, 87% coverage
Nwi_1364 Ribosomal protein L3 from Nitrobacter winogradskyi Nb-255
41% identity, 87% coverage
Q0E446 Large ribosomal subunit protein uL3c (Fragment) from Oryza sativa subsp. japonica
41% identity, 71% coverage
Q9SKX4 Large ribosomal subunit protein uL3c from Arabidopsis thaliana
AT2G43030 ribosomal protein L3 family protein from Arabidopsis thaliana
44% identity, 72% coverage
- Proteome and Interactome Linked to Metabolism, Genetic Information Processing, and Abiotic Stress in Gametophytes of Two Woodferns
Ojosnegros, International journal of molecular sciences 2023 - “...RPL18 LARGE RIBOSOMAL SUBUNIT PROTEIN UL18C 20.9 7 1 3 7.35 10 57 Ribogenesis 24557-506_3_ORF2 Q9SKX4 RPL3A LARGE RIBOSOMAL SUBUNIT PROTEIN UL3C 29.3 14 2 9 5.37 10 121 Ribogenesis 139931-207_5_ORF1 O04603 RPL5 LARGE RIBOSOMAL SUBUNIT PROTEIN UL5C 32.4 8 2 14 2.41 10 92 Ribogenesis...”
- iTRAQ-Based Quantitative Proteome Revealed Metabolic Changes in Winter Turnip Rape (Brassica rapa L.) under Cold Stress
Xu, International journal of molecular sciences 2018 - “...Fold Changes a L7TR/L7CK T4TR/T4CK L7TR/T4TR Ribosome Q9LY66 50S ribosomal protein L1 - - 0.348519904 Q9SKX4 50S ribosomal protein L3-1 - 0.636134306 0.365801714 Q9SLF7 60S acidic ribosomal protein P2-2 - - 0.483258248 Q8LD46 60S ribosomal protein L23a-1 - - 0.352601546 P36210 50S ribosomal protein L12-1 -...”
- Role of NPR1 in Systemic Acquired Stomatal Immunity
Guan, Plants (Basel, Switzerland) 2023 - “...0.02 3.95 AT4G35090 Catalase 2 0.02 3.94 AT2G40510 Ribosomal protein S26e family protein 0.01 3.80 AT2G43030 Ribosomal protein L3 family protein 0.02 3.73 AT3G02080 Ribosomal protein S19e family protein 0.01 3.60 AT1G26910 Ribosomal protein L16p/L10e family protein 0.01 3.42 AT5G15200 Ribosomal protein S4 0.01 3.28 AT4G18100...”
- Comprehensive proteomic and metabolomic analysis uncover the response of okra to drought stress
Wang, PeerJ 2022 - “...occupied the central position. In the P4 versus P1 network, the PRPL3 protein encoded by AT2G43030 had degree value of 184, the largest in the network. The CDC5 protein had the highest BC value in P4 versus P1, and in P5 versus P1. These results indicate...”
- “...f 0.04926569 13 NDPK2 0.04680682 13 AT1G12230 0.0442739 15 LOS2 0.04314511 15 rps15 0.04216912 16 AT2G43030 0.03732062 24 PP2AA2 0.03569743 11 GAPC1 d 0.03315947 13 P3 versus P1 CDC5 c 0.14663404 40 Hsp70b 0.10052988 38 TPI a 0.05953945 41 PSP 0.04886272 16 AT3G29320 b 0.0481939 21...”
- Plastid ribosome protein L5 is essential for post-globular embryo development in Arabidopsis thaliana
Dupouy, Plant reproduction 2022 - “...); Lloyd and Meinke ( 2012 ) L2 Essential ATCG00830/ ATCG01310 NA NA L3 Essential AT2G43030 NA NA L4 Essential AT1G07320 Essential Muralla et al. ( 2011 ); Lloyd and Meinke ( 2012 ) L5 Essential AT4G01310 Essential This Study L6 Essential AT1G05190 Essential Hsu et...”
- Changes in Brassica oleracea Leaves Infected With Xanthomonas campestris pv. campestris by Proteomics Analysis
Tortosa, Frontiers in plant science 2021 - “...L12-A RPL12-A M4E948 AT3G27830 1.5E-06 1.22 40.8 88 Ribosomal protein L3 family protein BRA000285 M4C7V7 AT2G43030 0.001 1.23 39.9 Glucosinolates degradation/myrosinase 82 * GDSL-like lipase/acylhydrolase superfamily protein N/A Q39308 AT1G54020 0.004 1.31 29 Redox state 46 * hiGh cyclic electron flow 1 FBP/HCEF1 P25851 AT3G54050 0.011...”
- Separation and Paired Proteome Profiling of Plant Chloroplast and Cytoplasmic Ribosomes
Firmino, Plants (Basel, Switzerland) 2020 - “...NA AT3G63490 plastid 50S uL1c RPL1 + NA ATCG01310 plastid 50S uL2c RPL2.2 + NA AT2G43030 plastid 50S uL3c RPL3 related + NA AT1G07320 plastid 50S uL4c RPL4 + NA AT4G01310 plastid 50S uL5c RPL5 family + NA AT1G05190 plastid 50S uL6c RPL6/emb2394 + NA AT3G44890...”
- The Arabidopsis Proteins AtNHR2A and AtNHR2B Are Multi-Functional Proteins Integrating Plant Immunity With Other Biological Processes
Singh, Frontiers in plant science 2020 - “...metabolism Figueroa et al., 2002 At2g27100 SERRATE (AtSE) Nucleus Alternative splicing Raczynska et al., 2014 At2g43030 L3-type protein of large ribosomal subunit Chloroplast Protein synthesis Kleffmann et al., 2004 At2g43610 Class-IV chitinase-like protein Extracellular space Plant immunity Kumar et al., 2018 At3g11430 Glycerol-3-phosphate acyltransferase (AtGPAT5) Endoplasmic...”
- Erythromycin Treatment of Brassica campestris Seedlings Impacts the Photosynthetic and Protein Synthesis Pathways
Yoon, Life (Basel, Switzerland) 2020 - “...M4D384 26 kDa 4.8 0.0 Bra010937 AT1G27450 Adenine phosphoribosyltransferase M4C7V7 29 kDa 4.1 0.0 Bra000285 AT2G43030 Ribosomal protein L3 family protein M4DCB8 19 kDa 4.1 0.0 Bra014131 AT1G48350 Ribosomal protein L18 family protein M4DJ77 26 kDa 4.1 0.0 Bra016555 AT1G18540 Ribosomal_L6e_N domain-containing protein M4CPV9 19 kDa...”
- Transcriptional analysis of sweet orange trees co-infected with 'Candidatus Liberibacter asiaticus' and mild or severe strains of Citrus tristeza virus
Fu, BMC genomics 2017 - “...putative / PSRP-3 1.40 RPS30A orange1.1g020955m AT5G24490 30S ribosomal protein, putative 1.09 1.39 RPL3 orange1.1g023905m AT2G43030 ribosomal protein L3 family protein 1.64 RPL5 orange1.1g024440m AT4G01310 ribosomal protein L5 family protein 1.69 RPL6 orange1.1g027306m AT1G05190 embryo defective 2394 1.58 RPL9 orange1.1g029153m AT3G44890 ribosomal protein L9 1.81 RPL10...”
- More
AT3G17465 RPL3P (RIBOSOMAL PROTEIN L3 PLASTID); structural constituent of ribosome from Arabidopsis thaliana
39% identity, 64% coverage
M4C7V7 Large ribosomal subunit protein uL3c from Brassica campestris
42% identity, 73% coverage
6z1pAd / Q22HG3 6z1pAd (see paper)
39% identity, 56% coverage
TP0189 ribosomal protein L3 (rplC) from Treponema pallidum subsp. pallidum str. Nichols
TPANIC_0189 50S ribosomal protein L3 from Treponema pallidum subsp. pallidum str. Nichols
36% identity, 94% coverage
- Antimicrobial susceptibility of Treponema pallidum subspecies pallidum: an in-vitro study
Tantalo, The Lancet. Microbe 2023 - “...ribosomal proteins, have been established as a linezolid resistance mechanism. 15 These targets correspond to tp0189 (L3) , tp0190 (L4), and tp0194 (L22) in T pallidum genes. Sequencing of the SS14 strain propagated in subtherapeutic linezolid concentrations did not have any genetic differences compared with the...”
- Comparison of transcriptional profiles of Treponema pallidum during experimental infection of rabbits and in vitro culture: Highly similar, yet different
De, PLoS pathogens 2021 - “...and modification 112 227 1.05 4.72E-07 TPANIC_0746 ppdK Energy metabolism; Glycolysis/gluconeogenesis 12,502 25,682 1.05 1.31E-11 TPANIC_0189 rplC Translation; Ribosomal proteins: Synthesis and modification 672 1,372 1.09 6.66E-13 TPANIC_0001 dnaA DNA metabolism; DNA replication, recombination and repair 297 628 1.09 2.81E-13 TPANIC_0870 flaB3 Cell envelope; Surface structures...”
AFUA_4G06000 mitochondrial 54S ribosomal protein uL3m from Aspergillus fumigatus Af293
38% identity, 69% coverage
RM09_YEAST / P31334 Large ribosomal subunit protein uL3m; 54S ribosomal protein L9, mitochondrial; YmL9 from Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast) (see 6 papers)
YGR220C Mitochondrial ribosomal protein of the large subunit from Saccharomyces cerevisiae
36% identity, 77% 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 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. - Systematic analysis of nuclear gene function in respiratory growth and expression of the mitochondrial genome in S. cerevisiae
Stenger, Microbial cell (Graz, Austria) 2020 - “...MNE1 YOR350C MRPL7 YDR237W RSM18 YER050C MRF1 YGL143C MRPL8 YJL063C RSM19 YNR037C MRP1 YDR347W MRPL9 YGR220C RSM22 YKL155C MRP10 YDL045W-A MRPS12 YNR036C RSM23 YGL129C MRP17 YKL003C MRPS16 YPL013C RSM24 YDR175C MRP20 YDR405W MRPS28 YDR337W RSM27 YGR215W MRP21 YBL090W MRPS5 YBR251W RSM7 YJR113C MRP4 YHL004W MRPS8 YMR158W...”
- “...IFM1 YOL023W MRPL38 YKL170W PET112 YBL080C IMG2 YCR071C MRPL6 YHR147C QRI5 YLR204W MHR1 YDR296W MRPL9 YGR220C RSM7 YJR113C MRF1 YGL143C MRPS5 YBR251W MRM1 YOR201C MSE1 YOL033W Respiratory chain components and assembly factors ATP15 YPL271W ATP7 YKL016C ATP17 YDR377W SDH4 YDR178W Other mitochondrial function ACO2 YJL200C MIS1...”
- Predicting essential proteins by integrating orthology, gene expressions, and PPI networks
Zhang, PloS one 2018 - “...increased cold sensitivity, decreased nuclear export, protein/peptide accumulation, and transposable element transposition [ 24 ]. YGR220C (MRPL9) is component of the large subunit of the mitochondrial ribosomal, which mediates translation in the mitochondrion; null causes absent respiratory growth, decreased competitive fitness [ 24 ]. YDR012W (RPL4B,...”
- Dosage Mutator Genes in Saccharomyces cerevisiae: A Novel Mutator Mode-of-Action of the Mph1 DNA Helicase
Ang, Genetics 2016 - “...CTF18 YHR164C DNA2 YKL204W EAP1 YDR434W GPI17 YDR378C LSM6 YLR274W MCM5 YNL173C MDG1 YIR002C MPH1 YGR220C MRPL9 YKR087C OMA1 YPR162C ORC4 YML061C PIF1 YLR196W PWP1 YML032C RAD52 YGL163C RAD54 YDR004W RAD57 YBR087W RFC5 YGL044C RNA15 YBR181C RPS6B YHR031C RRM3 YBR130C SHE3 YFL008W SMC1 YGL207W SPT16 YML010W...”
- Filtering Gene Ontology semantic similarity for identifying protein complexes in large protein interaction networks
Wang, Proteome science 2012 - “...YPL151C YML049C YLL036C - GO:0000398 2.35e-19 GO:0000384 2.04e-14 GO:0005681 5.52e-21 8 YNL252C YML025C YDR116C YNL284C YGR220C YCR046C - GO:0032543 2.74e-7 GO:0003735 2.16e-9 GO:0000315 1.05e-12 Figure 8 Topology of complex number 6, 7 and 8 in Table 5 . Conclusions Computational approaches for protein complex detection are...”
- Rif2 promotes a telomere fold-back structure through Rpd3L recruitment in budding yeast
Poschke, PLoS genetics 2012 - “...LYS14 YDR034C +++ HIT1 YJR055W + D RPB9 YGL070C +++ C Unknown YJR119C +++ MRPL9 YGR220C + BUD31 YCR063W +++ NPC2 YDL046W +++ VTC3 YPL019C + CTK1 YKL139W +++ C RTG3 YBL103C +++ MSR1 YHR091C + SIN3 YOL004W +++ B,C TPM2 YIL138C +++ EDE1 YBL047C +...”
- Efficient Tor signaling requires a functional class C Vps protein complex in Saccharomyces cerevisiae
Zurita-Martinez, Genetics 2007 - “...YOR150W YHR091C YKL170W YBR146W YNR037C YIL093C YBR268W YGR220C YKL138C YNL284C Mitochondrial function MDJ1 MRP51 MRPL24 MRPS16 MRPL8 IMG1 YLR426W MSM1 MRPL51...”
- Substrate specificity analysis of protein kinase complex Dbf2-Mob1 by peptide library and proteome array screening
Mah, BMC biochemistry 2005 - “...0.3592 YGL245W 0.2863 YIL010W DOT5 0.2606 YNL007C SIS1 0.2239 YHL021C 0.2094 YMR196W 0.2089 YJR142W 0.2005 YGR220C MRPL9 0.1976 YLR177W 0.1626 YJL211C 0.1594 YML035C AMD1 0.1384 YGL105W ARC1 0.1332 YGR264C MES1 0.1328 YPL257WA 0.1302 YBL024W NCL1 0.1294 YJR094WA 0.1141 YLR007W NSE1 0.0988 YLR303W MET17 0.0985 YGR223C 0.0837...”
- Mitochondrial ribosomal proteins (MRPs) of yeast
Graack, The Biochemical journal 1998 - “...location Total Signal peptide Daa P12687 S54026 P36517 S54533 SC8337 P22353 P31334 Z71560 Z74250 Q02204 S50921 S72159 14L 13R 12R 4R 13 10L 7 14 4 11 13R 12 371...”
3j6bC / P31334 of the yeast mitochondrial large ribosomal subunit (see paper)
36% identity, 84% coverage
RM09_SCHPO / Q9P6P6 Large ribosomal subunit protein uL3m; 54S ribosomal protein L9, mitochondrial from Schizosaccharomyces pombe (strain 972 / ATCC 24843) (Fission yeast) (see paper)
36% identity, 80% 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 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.
6yweC / Q873B3 structure of the mitoribosome from Neurospora crassa in the P/E tRNA bound state (see paper)
38% identity, 68% coverage
RM09_NEUCR / Q1K8T6 Large ribosomal subunit protein uL3m from Neurospora crassa (strain ATCC 24698 / 74-OR23-1A / CBS 708.71 / DSM 1257 / FGSC 987) (see 2 papers)
38% identity, 54% 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.
8c93D / P60438 Cryo-em captures early ribosome assembly in action (see paper)
36% identity, 94% coverage
4v61BF 4v61BF (see paper)
41% identity, 69% coverage
APH_0280 ribosomal protein L3 from Anaplasma phagocytophilum HZ
34% identity, 92% coverage
TGME49_230050 50S ribosomal protein L3, putative from Toxoplasma gondii ME49
35% identity, 40% coverage
- Identification of the Toxoplasma gondii mitochondrial ribosome, and characterisation of a protein essential for mitochondrial translation
Lacombe, Molecular microbiology 2019 - “...TGME49_251950 LSU Gupta et al. ( 2014 ) Strep 0.9672 0.08 3.60 Yes Tg uL3m TGME49_230050 LSU Gupta et al. ( 2014 ) FLAG 0.8966 0.02 4.50 Yes Tg uS15m TGME49_216040 SSU Gupta et al. ( 2014 ) N/A 0.9885 0.83 4.51 Yes Putative mitoribosomal proteins...”
- “...al. , 2014 ) via endogenous tagging: TgbL12m (TGME49_251950) was tagged with TwinStrep, and TguL3m (TGME49_230050) was tagged with tripleFLAG (Table 1 ); and confirmed their mitochondrial localizations (Fig. 1 B). Like TgmS35, under denaturing conditions these proteins migrate at the expected size of their mature...”
G3V7P3 Large ribosomal subunit protein uL3m from Rattus norvegicus
30% identity, 61% coverage
jhp1239 50S RIBOSOMAL PROTEIN L3 from Helicobacter pylori J99
30% identity, 92% coverage
HP1319 ribosomal protein L3 (rpl3) from Helicobacter pylori 26695
P56031 Large ribosomal subunit protein uL3 from Helicobacter pylori (strain ATCC 700392 / 26695)
30% identity, 92% coverage
Q99N95 Large ribosomal subunit protein uL3m from Mus musculus
29% identity, 61% coverage
7of0E / P09001 Structure of a human mitochondrial ribosome large subunit assembly intermediate in complex with mterf4-nsun4 (dataset1). (see paper)
30% identity, 67% coverage
RM03_HUMAN / P09001 Large ribosomal subunit protein uL3m; 39S ribosomal protein L3, mitochondrial; L3mt; MRP-L3 from Homo sapiens (Human) (see 5 papers)
NP_009139 large ribosomal subunit protein uL3m from Homo sapiens
30% identity, 59% coverage
- subunit: Component of the mitochondrial large ribosomal subunit (mt- LSU) (PubMed:25278503, PubMed:25838379, PubMed:28892042, PubMed:35177605). Mature mammalian 55S mitochondrial ribosomes consist of a small (28S) and a large (39S) subunit. The 28S small subunit contains a 12S ribosomal RNA (12S mt-rRNA) and 30 different proteins. The 39S large subunit contains a 16S rRNA (16S mt-rRNA), a copy of mitochondrial valine transfer RNA (mt-tRNA(Val)), which plays an integral structural role, and 52 different proteins.
- Targeted Delivery of Geraniol via Hyaluronic Acid-Conjugation Enhances Its Anti-Tumor Activity Against Prostate Cancer.
Yu, International journal of nanomedicine 2024 - “...ATP5F1A 13 O96008 Mitochondrial import receptor subunit TOM40 homolog TOMM40 12 P02768 Albumin ALB 12 P09001 39S ribosomal protein L3, mitochondrial MRPL3 12 Q5T653 39S ribosomal protein L2, mitochondrial MRPL2 12 Q9NRX2 39S ribosomal protein L17, mitochondrial MRPL17 12 P06576 ATP synthase subunit beta, mitochondrial ATP5F1B...”
- Proteomic distinction of renal oncocytomas and chromophobe renal cell carcinomas.
Drendel, Clinical proteomics 2018 - “...0.18 1.17 0.01 P30042 ES1 protein homolog, mitochondrial (Protein GT335) (Protein KNP-I) 0.44 0.90 0.01 P09001 39S ribosomal protein L3, mitochondrial (L3mt) (MRP-L3) (Mitochondrial large ribosomal subunit protein uL3m) 0.80 0.55 0.01 Q15067 Peroxisomal acyl-coenzyme A oxidase 1 (AOX) (EC 1.3.3.6) (Palmitoyl-CoA oxidase) (Straight-chain acyl-CoA oxidase)...”
- Biological pathways modulated by antipsychotics in the blood plasma of schizophrenia patients and their association to a clinical response.
Martins-de-Souza, NPJ schizophrenia 2015 - “...Up 1.254 5 Inter-alpha-trypsin inhibitor heavy chain H3 Protein metabolism Protease inhibitor Protease inhibitor activity P09001 RM03_HUMAN MRPL3 28 38,893 0.27 Down 1.813 2 39S ribosomal protein L3, mitochondrial Protein metabolism Ribosomal subunit Structural constituent of ribosome P01011 AACT_HUMAN SERPINA3 1317 47,792 1.48 Up 1.282 34...”
- Comparison of functional proteomic analyses of human breast cancer cell lines T47D and MCF7
Aka, PloS one 2012 - “...nuclear ribonucleoproteins A2/B1 P22626 35/37 5.8 3 Pre-mRNA processing http://www.uniprot.org/keywords/KW-0508 39S ribosomal protein L3, mitochondrial P09001 35/39 5.8 2 Translation 2685 U Cathepsin D (2658,2873,2674,2682,4384,4375,1968) P07339 28/45 5.0 20 Proteolysis cDNA, FLJ92320, highly similar to Homo sapiens glutathione S-transferase theta 2 (GSTT2), mRNA B2R533 28/28 5.0...”
- Comparison of cellular ribonucleoprotein complexes associated with the APOBEC3F and APOBEC3G antiviral proteins.
Gallois-Montbrun, Journal of virology 2008 - Comparative proteomic analysis of PAI-1 and TNF-alpha-derived endothelial microparticles.
Peterson, Proteomics 2008 - Analysis of the MRPL3, DNAJC13 and OFCC1 variants in Chinese Han patients with TS-CTD.
Guo, Neuroscience letters 2012 (PubMed)- GeneRIF: Found MRPL3 S75N variant is probably a rare cause of Tourette syndrome/chronic tic phenotype in Chinese Han patients.
- Exome sequencing identifies MRPL3 mutation in mitochondrial cardiomyopathy.
Galmiche, Human mutation 2011 (PubMed)- GeneRIF: the first mutation in large mitochondrial ribosomal protein MRPL3 in a family of four sibs with hypertrophic cardiomyopathy, psychomotor retardation, and multiple respiratory chain deficiency.(MRPL3)
- Genetic variants in nuclear-encoded mitochondrial genes influence AIDS progression.
Hendrickson, PloS one 2010 - GeneRIF: Observational study of gene-disease association. (HuGE Navigator)
Cj1707c 50S ribosomal protein L3 from Campylobacter jejuni subsp. jejuni NCTC 11168
38% identity, 52% coverage
RM03_BOVIN / Q3ZBX6 Large ribosomal subunit protein uL3m; 39S ribosomal protein L3, mitochondrial; L3mt; MRP-L3 from Bos taurus (Bovine) (see 2 papers)
29% identity, 61% coverage
- subunit: Component of the mitochondrial ribosome large subunit (39S) which comprises a 16S rRNA and about 50 distinct proteins.
W5PHI1 Large ribosomal subunit protein uL3m from Ovis aries
28% identity, 58% coverage
5aj4BE of the 55S mammalian mitoribosome. (see paper)
29% identity, 67% coverage
B4DKM0 Large ribosomal subunit protein uL3m from Homo sapiens
30% identity, 55% coverage
4v4pAE structure of 70S ribosome with thrS operator and tRNAs. (see paper)
27% identity, 94% coverage
7po4E / P09001 7po4E (see paper)
27% identity, 72% coverage
O26110 Large ribosomal subunit protein uL3 from Methanothermobacter thermautotrophicus (strain ATCC 29096 / DSM 1053 / JCM 10044 / NBRC 100330 / Delta H)
MTH2 ribosomal protein L3 (E.coli L3) from Methanothermobacter thermautotrophicus str. Delta H
27% identity, 36% coverage
- Archaeal aminoacyl-tRNA synthetases interact with the ribosome to recycle tRNAs
Godinic-Mikulcic, Nucleic acids research 2014 - “...homologue) b O27717, MTH1681 37 L12p (P1 homologue) b D9PUH1, MTH1682 11 ArgRS L3p b O26110, MTH2 37 L10 (P0 homologue) b O27717, MTH1681 37 EF-G b O27131, MTH1057 81 a Results obtained in experiment using 50S ribosomal subunit b Results obtained in experiment using 70S...”
- Archaeal aminoacyl-tRNA synthetases interact with the ribosome to recycle tRNAs
Godinic-Mikulcic, Nucleic acids research 2014 - “...b O27717, MTH1681 37 L12p (P1 homologue) b D9PUH1, MTH1682 11 ArgRS L3p b O26110, MTH2 37 L10 (P0 homologue) b O27717, MTH1681 37 EF-G b O27131, MTH1057 81 a Results obtained in experiment using 50S ribosomal subunit b Results obtained in experiment using 70S ribosomal...”
8hkuAL3P / Q4JB40 8hkuAL3P (see paper)
29% identity, 37% coverage
MMP1543 LSU Ribosomal protein L3P from Methanococcus maripaludis S2
29% identity, 32% coverage
RL3_HALMA / P20279 Large ribosomal subunit protein uL3; 50S ribosomal protein L3; Hl1; Hmal3 from Haloarcula marismortui (strain ATCC 43049 / DSM 3752 / JCM 8966 / VKM B-1809) (Halobacterium marismortui) (see 2 papers)
HISP_10980 50S ribosomal protein L3 from Haloarcula hispanica N601
rrnAC1611 50S ribosomal protein L3 from Haloarcula marismortui ATCC 43049
27% identity, 36% coverage
- function: One of the primary rRNA binding proteins, it binds directly near the 3'-end of the 23S rRNA, where it nucleates assembly of the 50S subunit.
subunit: Part of the 50S ribosomal subunit. Forms a cluster with proteins L14 and L24e. Interacts weakly with protein L13. - Insights into gene regulation of the halovirus His2 infecting Haloarcula hispanica
Lee, MicrobiologyOpen 2020 - “...AND PROCESSING Translation, ribosomal structure and biogenesis Ribosomal protein L14 0.321 0.683 1.313 0.309 M HISP_10980 INFORMATION STORAGE AND PROCESSING Translation, ribosomal structure and biogenesis Ribosomal protein L3 0.732 1.554 0.849 0.026 M HISP_04735 METABOLISM Amino acid transport and metabolism Glutamate synthase domain 2 0.292 0.572...”
- Metabolic capabilities and systems fluctuations in Haloarcula marismortui revealed by integrative genomics and proteomics analyses
Chu, Journal of proteome research 2011 - “...ribosomal protein L10e 14 7 2.0 rrnAC1592 rps5p 30S ribosomal protein S5P 63 35 1.8 rrnAC1611 rpl3p 50S ribosomal protein L3P 91 57 1.6 rrnAC0064 rpl18e 50S ribosomal protein L18e 41 26 1.6 rrnAC1595 rpl32e 50S ribosomal protein L32e 8 5 1.6 rrnAC1426 rps15p 30S ribosomal...”
3cc2B / P20279 The refined crystal structure of the haloarcula marismortui large ribosomal subunit at 2.4 angstrom resolution with rrna sequence for the 23s rrna and genome-derived sequences for r-proteins (see paper)
27% identity, 36% coverage
Ta1271 50S ribosomal protein L3 related protein from Thermoplasma acidophilum DSM 1728
Q9HIQ9 Large ribosomal subunit protein uL3 from Thermoplasma acidophilum (strain ATCC 25905 / DSM 1728 / JCM 9062 / NBRC 15155 / AMRC-C165)
27% identity, 34% coverage
Q9HPD4 Large ribosomal subunit protein uL3 from Halobacterium salinarum (strain ATCC 700922 / JCM 11081 / NRC-1)
26% identity, 35% coverage
For advice on how to use these tools together, see
Interactive tools for functional annotation of bacterial genomes.
The PaperBLAST database links 798,070 different protein sequences to 1,261,478 scientific articles. Searches against EuropePMC were last performed on May 12 2025.
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.
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.
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.
by Morgan Price,
Arkin group
Lawrence Berkeley National Laboratory