PaperBLAST

PaperBLAST Hits for 59 a.a. (MAKLEITLKR...)

Show query sequence

>59 a.a. (MAKLEITLKR...)
MAKLEITLKRSVIGRPEDQRVTVRTLGLKKTNQTVVHEDNAAIRGMINKVSHLVSVKEQ

Running BLASTp...

Found 73 similar proteins in the literature:

RL30_BACSU / P19947 Large ribosomal subunit protein uL30; 50S ribosomal protein L30; BL27 from Bacillus subtilis (strain 168) (see paper)
BSU01340 50S ribosomal protein L30 from Bacillus subtilis subsp. subtilis str. 168
100% identity, 100% coverage

• subunit: Part of the 50S ribosomal subunit.
• The Blueprint of a Minimal Cell: MiniBacillus
  Reuß, Microbiology and molecular biology reviews : MMBR 2016
  • “...BSU01210 BSU01180 BSU01270 BSU27940 BSU15820 BSU01240 BSU01340 BSU37070 BSU15080 BSU24900 BSU00990 BSU41060 BSU28860 BSU01400 BSU16490 BSU01220 BSU29660...”
• Proteomics analyses of Bacillus subtilis after treatment with plumbagin, a plant-derived naphthoquinone
  Reddy, Omics : a journal of integrative biology 2015
  • “...protein L27 OS P42920 50S ribosomal protein L3 OS P19947 50S ribosomal protein L30 OS O34967 50S ribosomal protein L31 type B OS P55874 50S ribosomal protein...”

7aqcZ / P19947 Structure of the bacterial rqc complex (decoding state) (see paper)
100% identity, 98% coverage

• Ligand: rna (7aqcZ)

lmo2614 ribosomal protein L30 from Listeria monocytogenes EGD-e
Q71WG4 Large ribosomal subunit protein uL30 from Listeria monocytogenes serotype 4b (strain F2365)
78% identity, 98% coverage

• Whole genome genetic variation and linkage disequilibrium in a diverse collection of Listeria monocytogenes isolates
  Louha, PloS one 2021
  • “...subunit ribosomal protein L32 lmo2628 rpsS 1508 67.56 2702909..2703187 accessory small subunit ribosomal protein S19 lmo2614 rpmD 1580 70.79 2697267..2697446 core large subunit ribosomal protein L30 lmo0758 - 1606 71.95 783901..784788 core Hypothetical protein lmo0514 - 1699 76.12 547520..549337 accessory Internalin lmo0305 - 1709 76.57 329923..330999...”
  • “..., lmo1469 , lmo2616 , lmo1816 , lmo0248 , lmo1335 , lmo2047 , lmo2628 , lmo2614 ), encode ribosomal proteins and their related subunits. According to the complexity theory [ 45 ], informational genes involved in complex biosystems and maintenance of basal cellular functions are usually...”
• Transcriptomic and Phenotypic Analyses of the Sigma B-Dependent Characteristics and the Synergism between Sigma B and Sigma L in Listeria monocytogenes EGD-e
  Mattila, Microorganisms 2020
  • “...L20 1.5 1.3 lmo2605 ribosomal protein L17 1.4 1.6 lmo2613 ribosomal protein L15 1.3 1.4 lmo2614 ribosomal protein L30 1.5 2 lmo2615 ribosomal protein S5 1.8 2 lmo2616 ribosomal protein L18 1.6 1.9 lmo2617 ribosomal protein L6 1.7 1.7 lmo2618 ribosomal protein S8 1.8 1.7 lmo2619...”
• Protein level identification of the Listeria monocytogenes sigma H, sigma L, and sigma C regulons
  Mujahid, BMC microbiology 2013
  • “...conditions tttcac atcgcagttagatgttt tatact SigmaA Lmo2487 1.65 hypothetical protein lmo2487 Hypothetical proteins Conserved N/A N/A Lmo2614 2.05 50S ribosomal protein L30 rpmD Protein synthesis Ribosomal proteins: synthesis and modification ttgatt actacccctaacccgtg tataat SigmaA Lmo2621 1.63 50S ribosomal protein L24 rplX Protein synthesis Ribosomal proteins: synthesis and...”
• Comparative analysis of the sigma B-dependent stress responses in Listeria monocytogenes and Listeria innocua strains exposed to selected stress conditions
  Raengpradub, Applied and environmental microbiology 2008
  • “...these genes are located in a 19-gene locus (lmo2614 to lmo2632). These data suggest that B indirectly controls transcription of L. monocytogenes genes involved...”
• Proteomic Exploration of Listeria monocytogenes for the Purpose of Vaccine Designing Using a Reverse Vaccinology Approach
  Srivastava, International journal of peptide research and therapeutics 2021
  • “...0.848 Non-allergen 132 Q720A8 0.628 Non-allergen 133 Q721Y1 0.988 Non-allergen 134 Q71YM9 1.733 Non-allergen 135 Q71WG4 2.217 Non-allergen 136 Q71YN4 2.371 Non-allergen 137 Q71WH3 2.224 Non-allergen 138 Q71ZY7 0.968 Non-allergen 139 Q71XW7 1.979 Non-allergen 140 Q720A1 0.577 Non-allergen 141 Q723G3 2.038 Non-allergen 142 Q71WV3 0.925 Non-allergen...”
  • “...DRB1_1301 VRVHAKVVE 67.1 1.564 Antigen DRB1_1301 RRGKVRRAK 20.2 1.3055 Antigen DRB1_1301 LRGKAARIK 17.4 2.0521 Antigen Q71WG4 DRB1_1301 AKLEITLKR 51.3 1.1423 Antigen Q71YN4 DRB1_0701 FKRTGSGKL 34.3 1.1993 Antigen DRB1_1301 THRGSAKRF 43.7 1.0624 Antigen DRB1_1301 QKQKRKLRK 46.1 1.1816 Antigen Q71WH3 DRB1_1301 LGRTSSQRK 33.5 1.2846 Antigen Q71ZY7 DRB1_1301 LKKYCPRLR...”

SAOUHSC_02493 ribosomal protein L30 from Staphylococcus aureus subsp. aureus NCTC 8325
A5IV16 Large ribosomal subunit protein uL30 from Staphylococcus aureus (strain JH9)
A8Z339 Large ribosomal subunit protein uL30 from Staphylococcus aureus (strain USA300 / TCH1516)
P0A0G0 Large ribosomal subunit protein uL30 from Staphylococcus aureus (strain N315)
Q2FEQ7 Large ribosomal subunit protein uL30 from Staphylococcus aureus (strain USA300)
Q6GEK1 Large ribosomal subunit protein uL30 from Staphylococcus aureus (strain MRSA252)
SA2030 50S ribosomal protein L30 from Staphylococcus aureus subsp. aureus N315
SACOL2221 ribosomal protein L30p/L7e from Staphylococcus aureus subsp. aureus COL
EKM74_RS05540, USA300HOU_RS12085 50S ribosomal protein L30 from Staphylococcus aureus subsp. aureus USA300_TCH1516
75% identity, 100% coverage

• Machine learning and network analysis with focus on the biofilm in <i>Staphylococcus aureus</i>
  Zhang, Computational and structural biotechnology journal 2024
  • “...and SAOUHSC_02559 ( ureB ), which are associated with nitrogen metabolism and urea degradation, alongside SAOUHSC_02493, a 50S ribosomal protein implicated in Staphylococcus aureus translation, as identified in a previous study [25] . SAOUHSC_00208 and SAOUHSC_00264 were denoted as coding for hypothetical proteins. Additionally, prominent genes,...”
• Antibacterial Components and Modes of the Methanol-Phase Extract from Commelina communis Linn
  Liu, Plants (Basel, Switzerland) 2023
  • “...0.492 Conserved hypothetical protein SAOUHSC_02860 3.217 HMG-CoA synthase putative Ribosome SAOUHSC_01191 0.258 Ribosomal protein L28 SAOUHSC_02493 0.326 Ribosomal protein L30 SAOUHSC_02494 0.353 Ribosomal protein S5 SAOUHSC_02499 0.358 Ribosomal protein S14p/S29e putative SAOUHSC_02504 0.360 Ribosomal protein L29 SAOUHSC_02492 0.369 Ribosomal protein L15 SAOUHSC_02498 0.383 Ribosomal protein S8...”
• A Carvacrol-Rich Essential Oil Extracted From Oregano (Origanum vulgare "Hot & Spicy") Exerts Potent Antibacterial Effects Against Staphylococcus aureus
  Hao, Frontiers in microbiology 2021
  • “...kinase A5ITM2 1.57 0.033 Up ATP-dependent 6-phosphofructokinase A5IV11 5.36 0.015 Up 50S ribosomal protein L36 A5IV16 1.97 0.001 Up 50S ribosomal protein L30 A7 0P6 0.64 0.034 Down UDP- N -acetylmuramoyl- L -alanyl- D -glutamate L -lysine ligase A8Z216 2.13 0.017 Up 50S ribosomal protein L33...”
• Antibacterial Activity and Multi-Targeted Mechanism of Action of Suberanilic Acid Isolated from Pestalotiopsis trachycarpicola DCL44: An Endophytic Fungi from Ageratina adenophora
  Wen, Molecules (Basel, Switzerland) 2024
  • “...protein VraR 0.816 Down 0.017176601 Translation A6QJ83 rpsQ 30S ribosomal protein S17 1.443 Up 0.023323817 A8Z339 rpmD 50S ribosomal protein L30 1.511 Up 0.010285859 Q6GJD4 rpmG3 50S ribosomal protein L33 3 0.555 Down 0.01660196 P66645 rpsI 30S ribosomal protein S9 1.272 Up 0.001495131 A0A850G4M4 rplC 50S...”
  • “...14 Q5HEP0 vraR 0.816 0.965351503 1.006 Consistency 15 A6QJ83 rpsQ 1.443 0.008784577 2.012 Consistency 16 A8Z339 rpmD 1.511 0.004055361 1.613 Consistency Note: Consistency....”
• Identification of N-terminal protein processing sites by chemical labeling mass spectrometry
  Misal, Rapid communications in mass spectrometry : RCM 2019
  • “...33 MA VISMKQLLEAGVHFGHQTR R P66544 Ribosomal protein S2 Cytoplasm 2 2 34 M AKLQITLTR S P0A0G0 Ribosomal protein L30 Cytoplasm 16 10 35 MA KLQITLTR S P0A0G0 Ribosomal protein L30 Cytoplasm 71 27 36 MA SLKSIIR Q Q7A7B3 Ribosomal protein L25 Cytoplasm 3 3 Table 2....”
• The Spl Serine Proteases Modulate Staphylococcus aureus Protein Production and Virulence in a Rabbit Model of Pneumonia
  Paharik, mSphere 2016
  • “...( RL31B_STAA3 ) 50S ribosomal protein L31 type B RpmE2 Housekeeping, translation 2.67 7.00 0.0096 Q2FEQ7 ( RL30_STAA3 ) 50S ribosomal protein L30 RpmD Housekeeping, translation 0.00 2.33 0.007 Q2FJU4 ( Q2FJU4_STAA3 ) Triacylglycerol lipase GehB/SAL2 Lipase 8.67 32.33 1.2E11 Q2FH26 ( ODO2_STAA3 ) Dihydrolipoyllysine residue...”
• Structural and Functional Dynamics of Staphylococcus aureus Biofilms and Biofilm Matrix Proteins on Different Clinical Materials
  Hiltunen, Microorganisms 2019
  • “...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 50S ribosomal protein L7/L12 Q6GJC8...”
• Analysis of the matrix-assisted laser desorption ionization-time of flight mass spectrum of Staphylococcus aureus identifies mutations that allow differentiation of the main clonal lineages
  Josten, Journal of clinical microbiology 2013
  • “...(SAOUHSC_02260) graF (SAS030) SAS049 rpmF (SAS033) rpmD (SA2030) SA1452 graC (SAS044) SA2039 rpsP (SA1081) Primer sequence SAS078for SAS078rev SAR1012for...”
  • “...SAS049 SAS049 SAS049 rpmF (SAS033) rpmF (SAS033) rpmD (SA2030) rpmD (SA2030) SA1452 SA1452 SA1452 SA1452 graC (SAS044) graC (SAS044) graC (SAS044) graC (SAS044)...”
• Transcriptional profiles of the response of methicillin-resistant Staphylococcus aureus to pentacyclic triterpenoids
  Chung, PloS one 2013
  • “...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 L32 7.7 Translation SAS042 rpmG 50S ribosomal protein...”
• Characterizing the effect of the Staphylococcus aureus virulence factor regulator, SarA, on log-phase mRNA half-lives
  Roberts, Journal of bacteriology 2006
  • “...SA2040 SA2022 SA2032 SA1084 SA2036 SA0459 SA1067 SA2039 SA2030 SAS042 SAS047 SA1308 SA2031 SA0352 SA0352 SA0504 SA2034 SA2024 SA0503 SA2025 SAS079 SA2038 SA1414...”
• Differential gene expression profiling of Staphylococcus aureus cultivated under biofilm and planktonic conditions
  Resch, Applied and environmental microbiology 2005
  • “...2.832 2.621 2.614 2.557 2.516 SA2016 SA2017 SA1471 SA2030 SA2045 SA1081 SA2029 SA0504 SA0495 SA1473 SA0354 SA0503 SA2031 SA0497 SA1116 SA2032 SA0496 3.324 3.241...”
• The Staphylococcus aureus LytSR two-component regulatory system affects biofilm formation
  Sharma-Kuinkel, Journal of bacteriology 2009
  • “...SACOL1702 SACOL2234 SACOL2237 SACOL2228 SACOL2231 SACOL2221 SACOL1726 SACOL1274 SACOL2233 SACOL2222 SACOL0592 SACOL2240 SACOL2214 SACOL0591 SACOL2226 SACOL1292...”
• Transcriptomic Analysis Revealed Antimicrobial Mechanisms of Lactobacillus rhamnosus SCB0119 against Escherichia coli and Staphylococcus aureus
  Peng, International journal of molecular sciences 2022
  • “...ribosomal protein L36 EKM74_RS05535 328.44 51.85 2770.35 239.31 3.076378 rplO ; 50S ribosomal protein L15 EKM74_RS05540 370.08 105.31 13,564.79 1089.74 5.195877 rpmD ; 50S ribosomal protein L30 EKM74_RS05545 183.9 22.05 4254.61 754.45 4.532035 rpsE ; 30S ribosomal protein S5 EKM74_RS05550 205.01 26.43 9035.82 328.78 5.461917 rplR...”
• Absence of Protoheme IX Farnesyltransferase CtaB Causes Virulence Attenuation but Enhances Pigment Production and Persister Survival in MRSA
  Xu, Frontiers in microbiology 2016
  • “...1.49 2.77E-02 Biotin carboxylase USA300HOU_RS12615 hutU 1.49 3.30E-02 Urocanate hydratase USA300HOU_RS13410 1.47 3.09E-02 Possible decarboxylase USA300HOU_RS12085 rpmD 1.46 2.95E-02 Ribosomal protein L30 USA300HOU_RS11770 1.46 3.46E-02 Hypothetical membrane protein USA300HOU_RS06545 glpK 1.45 3.79E-02 Glycerol kinase USA300HOU_RS03955 nrdF 1.45 3.80E-02 Ribonucleoside-diphosphate reductase subunit beta USA300HOU_RS12120 rplX 1.41 4.01E-02...”

BC_0149 50S ribosomal protein L30 from Bacillus cereus ATCC 14579
Q81VR2 Large ribosomal subunit protein uL30 from Bacillus anthracis
BC0149, NP_830029 LSU ribosomal protein L30P from Bacillus cereus ATCC 14579
77% identity, 93% coverage

• Proteomic evidences for rex regulation of metabolism in toxin-producing Bacillus cereus ATCC 14579
  Laouami, PloS one 2014
  • “...RplX BC_0142 NP_830022 50 S ribosomal protein L24 N N 2,2 0,03 0,79 0,154 RpmD BC_0149 NP_830029 50 S ribosomal protein L30 N N 1,03 0,095 2,4 0,02 Frr BC_3822 NP_833543 Ribosome recycling factor N N 1,6 0,04 0,23 0,405 RaiA BC_5190 NP_834854 SSU ribosomal protein...”
• Identification of Bacillus anthracis by using matrix-assisted laser desorption ionization-time of flight mass spectrometry and artificial neural networks
  Lasch, Applied and environmental microbiology 2009
  • “...Q81JG9 Q81Y79 Q81U79 Unassigned Q81LW9 Unassigned Unassigned Q6HUG3 Q81VR2 Unassigned 3,322 3,340 3,418 3,541 3,595 3,653 3,683 3,694 3,885 Q81LS7 Q81KU1 Q81UL0...”
  • “...Q81U86 Q81Y79 Q81U79 Q81LW9 Q81U56 Q6HUG3 Unassigned Q81VR2 Unassigned Q81LS7 Q81KU1 Q81UL0 Q81RQ3 Q81VR7 7,269 7,368 7,771 Q81WS1 Q81YF5 Q81V00 9,217...”
• Methionine Residues in Exoproteins and Their Recycling by Methionine Sulfoxide Reductase AB Serve as an Antioxidant Strategy in Bacillus cereus
  Madeira, Frontiers in microbiology 2017
  • “...2.80 NP_830829 BC1043 PrsA1 Peptidylprolyl isomerase 2.57 NP_834192 BC4480 Tig Trigger factor 2.14 Translation NP_830029 BC0149 RpmD 50S ribosomal protein L30 1.30 NP_833528 BC3806 RpsO 30S ribosomal protein S15 2.38 NP_830008 BC0128 FusA Elongation factor G 2.59 NP_830009 BC0129 Tuf Elongation factor Tu 2.79 2.95 Transcriptional...”
  • “...isomerase 2.80 NP_830829 BC1043 PrsA1 Peptidylprolyl isomerase 2.57 NP_834192 BC4480 Tig Trigger factor 2.14 Translation NP_830029 BC0149 RpmD 50S ribosomal protein L30 1.30 NP_833528 BC3806 RpsO 30S ribosomal protein S15 2.38 NP_830008 BC0128 FusA Elongation factor G 2.59 NP_830009 BC0129 Tuf Elongation factor Tu 2.79 2.95...”
• Proteomic evidences for rex regulation of metabolism in toxin-producing Bacillus cereus ATCC 14579
  Laouami, PloS one 2014
  • “...BC_0142 NP_830022 50 S ribosomal protein L24 N N 2,2 0,03 0,79 0,154 RpmD BC_0149 NP_830029 50 S ribosomal protein L30 N N 1,03 0,095 2,4 0,02 Frr BC_3822 NP_833543 Ribosome recycling factor N N 1,6 0,04 0,23 0,405 RaiA BC_5190 NP_834854 SSU ribosomal protein S30P...”

SERP1813 ribosomal protein L30 from Staphylococcus epidermidis RP62A
71% identity, 98% coverage

• Concentration-Dependent Global Quantitative Proteome Response of Staphylococcus epidermidis RP62A Biofilms to Subinhibitory Tigecycline
  Sung, Cells 2022
  • “...IF-1 2.91 3.65 4.95 SERP1812 rplO fig|176279.9.peg.1769 J 50S ribosomal protein L15 9.94 14.43 15.32 SERP1813 rpmD fig|176279.9.peg.1770 J 50S ribosomal protein L30 2.61 4.52 3.31 SERP1814 rpsE fig|176279.9.peg.1771 J 30S ribosomal protein S5 3.48 6.69 11.59 SERP1815 rplR fig|176279.9.peg.1772 J 50S ribosomal protein L18 7.10...”
  • “...L15 9.94 14.43 15.32 SERP0186 rpsL fig|176279.9.peg.177 J 30S ribosomal protein S12 1000.00 0.00 1000.00 SERP1813 rpmD fig|176279.9.peg.1770 J 50S ribosomal protein L30 2.61 4.52 3.31 SERP1814 rpsE fig|176279.9.peg.1771 J 30S ribosomal protein S5 3.48 6.69 11.59 SERP1815 rplR fig|176279.9.peg.1772 J 50S ribosomal protein L18 7.10...”
• Impact of the Staphylococcus epidermidis LytSR two-component regulatory system on murein hydrolase activity, pyruvate utilization and global transcriptional profile
  Zhu, BMC microbiology 2010
  • “...chain 2.036 SERP1809 infA translation initiation factor IF-1 0.5 SERP1812 rplO ribosomal protein L15 0.482 SERP1813 rpmD ribosomal protein L30 0.333 SERP1814 rpsE 30 S ribosomal protein S5 0.37 SERP1815 rplR 50 S ribosomal protein L18 0.323 SERP1816 rplF 50 S ribosomal protein L6 0.332 SERP1817...”

SE1805 50S ribosomal protein L30 from Staphylococcus epidermidis ATCC 12228
71% identity, 100% coverage

• Synergistic Microbicidal Effect of Auranofin and Antibiotics Against Planktonic and Biofilm-Encased S. aureus and E. faecalis
  She, Frontiers in microbiology 2019
  • “...SE1802 0.125 1 2 2 SE1803 0.125 0.5 2 2 SE1804 0.125 0.5 1 1 SE1805 0.125 1 2 4 SE1806 0.125 2 1 1 SE1807 0.125 1 2 2 SE1808 0.125 1 2 2 SE1809 b 0.125 0.5 2 4 SE1810 b 0.125 1 2...”

8a573 / Q927M5 Cryo-em structure of hflxr bound to the listeria monocytogenes 50s ribosomal subunit. (see paper)
77% identity, 95% coverage

• Ligand: rna (8a573)

7asmX / P0A0G2 Staphylococcus aureus 50s after 30 minutes incubation at 37c
74% identity, 98% coverage

• Ligand: rna (7asmX)

5nrgW / P0A0G2 The crystal structure of the large ribosomal subunit of staphylococcus aureus in complex with rb02 (see paper)
75% identity, 97% coverage

• Ligand: rna (5nrgW)

IUJ47_RS04615 50S ribosomal protein L30 from Enterococcus faecalis
Q839E6 Large ribosomal subunit protein uL30 from Enterococcus faecalis (strain ATCC 700802 / V583)
EF0225 ribosomal protein L30 from Enterococcus faecalis V583
64% identity, 98% coverage

• Antibacterial Components and Modes of the Methanol-Phase Extract from Commelina communis Linn
  Liu, Plants (Basel, Switzerland) 2023
  • “...ribosomal protein L15 IUJ47_RS04605 0.331 50S ribosomal protein L18 IUJ47_RS01025 0.344 50S ribosomal protein L10 IUJ47_RS04615 0.351 50S ribosomal protein L30 IUJ47_RS04610 0.353 30S ribosomal protein S5 IUJ47_RS07790 0.471 50S ribosomal protein L21 IUJ47_RS07070 2.015 50S ribosomal protein L25/general stress protein Ctc IUJ47_RS03860 4.258 50S ribosomal...”
• Effectiveness of Bioactive Compound as Antibacterial and Anti-Quorum Sensing Agent from Myrmecodia pendans: An In Silico Study
  Satari, Molecules (Basel, Switzerland) 2021
  • “...beta (UniProt ID: Q82Z41), ribosomal subunit 30S (UniProt ID: Q82ZI6), ribosomal subunit 50S (UniProt ID: Q839E6), FsrB (UniProt ID: G8ADN9), and GBAP (UniProt ID: G8ADP0). Meanwhile, the eight ligands considered were M. pendans compounds that were published in previous studies [ 31 , 32 , 33...”
  • “...beta (UniProt ID: Q82Z41), ribosomal subunit 30S (UniProt ID: Q82ZI6), ribosomal subunit 50S (UniProt ID: Q839E6), FsrB (UniProt ID: G8ADN9), and GBAP (UniProt ID: G8ADP0), which were built using the SWISS-MODEL server ( https://swissmodel.expasy.org/ , accessed on 8 May 2020) in PDB file format [ 42...”
• Transcriptome analysis of Enterococcus faecalis during mammalian infection shows cells undergo adaptation and exist in a stringent response state
  Frank, PloS one 2014
  • “...8 h microarray DOWN+RIVET antisense EF0005 DNA gyrase subunit B EF0013 replicative DNA helicase DnaB EF0225 50S ribosomal protein L30 EF0226 50S ribosomal protein L15 EF0724 glutamyl-tRNA(Gln) amidotransferase subunit C EF0801 leucyl-tRNA synthetase EF0909 oligopeptide ABC superfamily ATP binding cassette transporter, membrane protein EF0988 cell division...”
• Transcriptional response of Enterococcus faecalis V583 to erythromycin
  Aakra, Antimicrobial agents and chemotherapy 2005
  • “...EF0706 EF1310 EF1647 EF1700 EF2730 EF3073 EF0223 EF0224 EF0225 EF0226 EF0970 EF1694 EF2395 EF2397 EF2473 EF2474 EF2679 EF2731 EF3070 EF0285 EF1714 EF1718 EF2362...”

6o8w0 / A0A1B4XKW1 6o8w0 (see paper)
63% identity, 97% coverage

• Ligand: rna (6o8w0)

STER_RS09255 50S ribosomal protein L30 from Streptococcus thermophilus LMD-9
62% identity, 97% coverage

• Cell Proteins Obtained by Peptic Shaving of Two Phenotypically Different Strains of Streptococcus thermophilus as a Source of Anti-Inflammatory Peptides
  Allouche, Nutrients 2022
  • “...96.83 8 61.91 STER_1899|ID:1900562|rpmC| STER_RS09305 50S ribosomal subunit protein L29 7.90 Cyto 12 68.12 STER_1889|ID:1900552|rpmD| STER_RS09255 50S ribosomal subunit protein L30 6.39 Cyto 51 88.53 9 44.26 STER_1953|ID:1899670|rpmF| STER_RS09555 50S ribosomal subunit protein L32 6.78 Cyto 12 83.61 STER_1954|ID:1899671|rpmG| STER_RS09560 50S ribosomal subunit protein L33 5.92...”
  • “...STHERMOCNRZ21N_v1_10753|ID:59659903|livJ| Branched-chain amino acid ABC uptake transporter substrate-binding protein 41.81 CS/M 8 23.98 Translation STER_1889|ID:1900552|rpmD| STER_RS09255 50S ribosomal subunit protein L30 6.39 Cyto 9 44.26 10 57.38 STHERMOCNRZ21N_v1_31096|ID:59661236|rpmD| Ribosomal protein L30 (BL27) 6.39 Cyto 18 81.97 STER_0639|ID:1899231| STER_RS03135 40S ribosomal protein S1 43.88 Cyto 8 7.48...”

SUB0086 50S ribosomal protein L30 from Streptococcus uberis 0140J
57% identity, 97% coverage

• Prediction of Streptococcus uberis clinical mastitis treatment success in dairy herds by means of mass spectrometry and machine-learning
  Maciel-Guerra, Scientific reports 2021
  • “...12 different proteins (Table 4 ). Specifically, peak 6386.04Da could be matched to three proteins (SUB0086, SUB1598 and SUB0788), peak 8139.57Da could be matched to three proteins (SUB0956, SUB0512 and SUB0090) and peak 9487.76Da could be matched to two proteins (SUB1267 and SUB0408). While peaks 5377.47Da,...”
  • “...SUB0788) while ten proteins had known functions: four of them were 50S ribosomal proteins (SUB1659A, SUB0086, SUB1795 and SUB0076) two of them were 30S ribosomal proteins (SUB0689 and SUB0956), and the four remaining proteins were bacteriocin (SUB0512), translation initiation factor (SUB0090), DNA-binding (SUB1267), and a membrane...”

SPV_0211 50S ribosomal protein L30 from Streptococcus pneumoniae
SP_0228 50S ribosomal protein L30 from Streptococcus pneumoniae TIGR4
62% identity, 97% coverage

• Refining the Pneumococcal Competence Regulon by RNA Sequencing
  Slager, Journal of bacteriology 2019
  • “...1.1 0.8 0.2 SPV_0209 rplR 3,598 1.1 0.9 0.2 SPV_0210 rpsE 3,477 1.1 0.9 0.2 SPV_0211 rpmD 4,120 1.1 0.9 0.4 SPV_0212 rplO 2,247 1.2 0.7 0.2 SPV_0213 secY 1,920 1.0 0.7 0.3 a Boldface data indicate significance ( P <0.001; log 2 fold change [FC]...”
• Biofilm and planktonic pneumococci demonstrate disparate immunoreactivity to human convalescent sera
  Sanchez, BMC microbiology 2011
  • “...0 2 50S ribosomal protein L22 rplV (SP_0214) 0 6 50S ribosomal protein L30 rpmD (SP_0228) 0 2 Elongation factor G fusA (SP_0273) 10 72 Elongation factor P efp (SP_0435) 5 7 Elongation factor Ts tsf (SP_2214) 14 16 Elongation factor Tu (SP_0681) 29 59 Arginyl-tRNA...”

CAC3115 Ribosomal protein L30 from Clostridium acetobutylicum ATCC 824
60% identity, 97% coverage

• Complex and extensive post-transcriptional regulation revealed by integrative proteomic and transcriptomic analysis of metabolite stress response in Clostridium acetobutylicum
  Venkataramanan, Biotechnology for biofuels 2015
  • “...and pyrimidine metabolism. Other genes, which belong to this category, include two ribosomal proteins - CAC3115 ( rpmD ) and CAC1284 ( prmA ). Butanol stress inhibits cell growth, and it appears that a select set of ribosomal proteins are downregulated as a result of the...”

MSMEG_1473 ribosomal protein L30 from Mycobacterium smegmatis str. MC2 155
60% identity, 95% coverage

• Gene Expression, Bacteria Viability and Survivability Following Spray Drying of Mycobacterium smegmatis
  Lauten, Materials (Basel, Switzerland) 2010
  • “...L28 rpmB 1.5 12.8 0.000 99% MSMEG_1444 ribosomal protein L29 rpmC 1.8 11.8 0.013 14% MSMEG_1473 ribosomal protein L30 rpmD 1.5 11.9 0.001 95% MSMEG_4951 ribosomal protein L31 rpmE 0.8 13.8 0.005 37% MSMEG_5489 ribosomal protein L32 rpmF 1.1 11.1 0.010 22% MSMEG_6070 ribosomal protein L31...”

5zeb1 / A0QSG7 5zeb1 (see paper)
60% identity, 95% coverage

• Ligand: rna (5zeb1)

Q1GBK0 Large ribosomal subunit protein uL30 from Lactobacillus delbrueckii subsp. bulgaricus (strain ATCC 11842 / DSM 20081 / BCRC 10696 / JCM 1002 / NBRC 13953 / NCIMB 11778 / NCTC 12712 / WDCM 00102 / Lb 14)
55% identity, 95% coverage

• Effects of ccpA gene deficiency in Lactobacillus delbrueckii subsp. bulgaricus under aerobic conditions as assessed by proteomic analysis
  Zhang, Microbial cell factories 2020
  • “...32.43 58.31 2.174 A0A0D6ZH63 Amino acid ABC transporter permease 25.34 12.95 2.252 Genetic information processing Q1GBK0 50S ribosomal protein L30 6.67 60.66 3.435 Q04BZ9 50S ribosomal protein L18 12.92 73.95 2.171 Q71J17 50S ribosomal protein L22 10.58 68.37 2.147 G6F488 Ribosome maturation factor RimP 15.52 11.28...”

XNR_3747 50S ribosomal protein L30 from Streptomyces albidoflavus
52% identity, 97% coverage

• Insights into naturally minimised Streptomyces albus J1074 genome
  Zaburannyi, BMC genomics 2014
  • “...for the genes encoding ribosomal proteins S8 (XNR_3743), L6 (XNR_3744), L18 (XNR_3745), S5 (XNR_3746), L30 (XNR_3747) and L15 (XNR_3748) at 12, 36 and 60h after culture inoculation. Figure 6 Transcription levels of PhoPR regulatory system. Transcription levels measured in FPKM of XNR_5270 ( phoP ) and...”

LSEI_2485 Ribosomal protein L30 from Lactobacillus casei ATCC 334
53% identity, 95% coverage

• Physiological and transcriptional response of Lactobacillus casei ATCC 334 to acid stress
  Broadbent, Journal of bacteriology 2010
  • “...LSEI_2478 LSEI_2479 LSEI_2480 LSEI_2481 LSEI_2484 LSEI_2485 LSEI_2486 LSEI_2487 LSEI_2488 LSEI_2489 LSEI_2490 LSEI_2491 LSEI_2492 LSEI_2493 LSEI_2494 LSEI_2495...”

DU507_12850 50S ribosomal protein L30 from Lacticaseibacillus rhamnosus GG
53% identity, 95% coverage

• Ribosomal protein L4 of Lactobacillus rhamnosus LRB alters resistance to macrolides and other antibiotics
  Biswas, Molecular oral microbiology 2020
  • “...(DU507_12550) 04 54.5 54.50 AXI94936 ABC transporter (DU507_10780) 02 5.4 3.15 AXI95307 Ribosomal protein L30 (DU507_12850) 02 50.8 45.80 AXI93974 PHB domain protein (DU507_05405) 03 11.0 7.00 AXI95670 N-acetyltransferase (DU507_14915) 04 33.5 31.30 AXI94116 F0F1 ATP synthase (DU507_06210) 01 23.1 42.52 AXI93353 Beta-galactosidase (DU507_01720) 04 6.7...”

5myjB2 / A2RNN5 of 70S ribosome from Lactococcus lactis (see paper)
54% identity, 97% coverage

• Ligand: rna (5myjB2)

B7C60_RS03530 50S ribosomal protein L30 from Vibrio fujianensis
50% identity, 98% coverage

• Comparative Genomics and Transcriptomics Analyses Reveal a Unique Environmental Adaptability of Vibrio fujianensis
  Huang, Microorganisms 2020
  • “...rpmJ large subunit ribosomal protein L36 Translation B7C60_RS03525 rplO large subunit ribosomal protein L15 Translation B7C60_RS03530 rpmD large subunit ribosomal protein L30 Translation B7C60_RS03535 rpsE small subunit ribosomal protein S5 Translation B7C60_RS03540 rplR large subunit ribosomal protein L18 Translation B7C60_RS03545 rplF large subunit ribosomal protein L6...”

Bbr_1623 50S ribosomal protein L30 from Bifidobacterium breve UCC2003
51% identity, 95% coverage

• Genome-Wide Search for Genes Required for Bifidobacterial Growth under Iron-Limitation
  Lanigan, Frontiers in microbiology 2017
  • “...rpsH , 30S ribosomal protein S8 2.3 Bbr_1726 rlpA , LSU ribosomal protein L1P 2.3 Bbr_1623 rpmD , 50S ribosomal protein L30 2.2 Bbr_1628 rpsN , 30S ribosomal protein S14-1 2.2 Bbr_1626 rplF , 50S ribosomal protein L6 2.2 Bbr_1624 rpsE , 30S ribosomal protein S5...”

Cp1002_0374 50S ribosomal protein L30 from Corynebacterium pseudotuberculosis 1002
51% identity, 90% coverage

• An integrated structural proteomics approach along the druggable genome of Corynebacterium pseudotuberculosis species for putative druggable targets
  Radusky, BMC genomics 2015
  • “...D9Q838 Acetylglutamate kinase [ 33 ] 4 Cp1002_0412 D9Q6L7 Alanine racemase [ 34 ] 5 Cp1002_0374 D9Q6I0 50S ribosomal protein L30 [ 26 ] 6 Cp1002_1592 D9Q409 Bifunctional protein folC [ 35 ] 7 Cp1002_1239 D9Q8X6 Diaminopimelate epimerase [ 36 ] 8 Cp1002_1270 D9Q906 Riboflavin biosynthesis...”

MAB_3794c 50S ribosomal protein L30 from Mycobacterium abscessus ATCC 19977
52% identity, 97% coverage

• Genome-Wide Essentiality Analysis of Mycobacterium abscessus by Saturated Transposon Mutagenesis and Deep Sequencing
  Rifat, mBio 2021
  • “...Glutamyl-tRNA(Gln) amidotransferase subunit C GatC MAB_3772c 30S ribosomal protein S11 MAB_3793c 50S ribosomal protein L15 MAB_3794c 50S ribosomal protein L30 MAB_3804c 30S ribosomal protein S14P/S29E MAB_3812c 50S ribosomal protein L29 MAB_3991c Possible uroporphyrin-III C-methyltransferase MAB_4145 Probable ,-trehalose-phosphate synthase MAB_4953c Membrane protein OxaA MAB_4954c Ribonuclease P protein...”

VP0275 ribosomal protein L30 from Vibrio parahaemolyticus RIMD 2210633
48% identity, 98% coverage

• Rapid identification of Vibrio parahaemolyticus by whole-cell matrix-assisted laser desorption ionization-time of flight mass spectrometry
  Hazen, Applied and environmental microbiology 2009
  • “...P protein Hypothetical protein 50S ribosomal protein L17 VP0275 VP2529 VP0265 VP2335 VP2817 VP2331 VP0160 VP1210 VP0261 VPA0321 VPA0286 VP2627 VP2619 VP2029...”
  • “...Hypothetical protein 50S ribosomal protein L17 VP0082 VP0275 VP0186 VP2546 VP1210 VP0261 VPA1414 VP0273 VP2098 Transmembrane protein 50S ribosomal protein L30...”

FP1321 50S ribosomal protein L30 from Flavobacterium psychrophilum JIP02/86
53% identity, 97% coverage

• Stress Tolerance-Related Genetic Traits of Fish Pathogen Flavobacterium psychrophilum in a Mature Biofilm
  Levipan, Frontiers in microbiology 2018
  • “...GO:0019843, GO:0043022, GO:0006413 3.53 FP1320 50S ribosomal protein L15 rplO GO:0015934, GO:0003735, GO:0019843, GO:0006412 3.20 FP1321 50S ribosomal protein L30 rpmD GO:0015934, GO:0003735, GO:0006412 4.92 FP1322 30S ribosomal protein S5 rpsE GO:0015935, GO:0003735, GO:0019843, GO:0006412 2.91 FP1323 50S ribosomal protein L18 rplR GO:0005840, GO:0003735, GO:0019843, GO:0006412...”

SCO4720 50S ribosomal protein L30 from Streptomyces coelicolor A3(2)
50% identity, 97% coverage

• Comparative genomics of Streptomyces avermitilis, Streptomyces cattleya, Streptomyces maritimus and Kitasatospora aureofaciens using a Streptomyces coelicolor microarray system
  Hsiao, Antonie van Leeuwenhoek 2008
  • “...protein L18 0.09 0.30 0.57 0.74 SCO4719 30S ribosomal protein S5 1.56 0.66 1.02 0.09 SCO4720 50S ribosomal protein L30 0.13 0.39 0.64 0.26 SCO4721 50S ribosomal protein L15 1.79 0.42 0.80 0.84 SCO4726 50S ribosomal protein L36 0.46 0.13 0.35 0.10 SCO4727 30S ribosomal protein...”

BCG_0772 putative 50S ribosomal protein L30 rpmD from Mycobacterium bovis BCG str. Pasteur 1173P2
A1KGK3 Large ribosomal subunit protein uL30 from Mycobacterium bovis (strain BCG / Pasteur 1173P2)
P9WHA3 Large ribosomal subunit protein uL30 from Mycobacterium tuberculosis (strain ATCC 25618 / H37Rv)
MT0747 50S ribosomal protein L30 from Mycobacterium tuberculosis CDC1551
Rv0722 50S ribosomal protein L30 from Mycobacterium tuberculosis H37Rv
MRA_0730 50S ribosomal protein L30 from Mycobacterium tuberculosis H37Ra
51% identity, 88% coverage

• InbR, a TetR family regulator, binds with isoniazid and influences multidrug resistance in Mycobacterium bovis BCG
  Yang, Scientific reports 2015
  • “...50S ribosomal protein L29 Up BCG_0760 1.79 1.94 Rv0710 rpsQ 30S ribosomal protein S17 9 BCG_0772 1.64 1.52 Rv0722 rpmD 50S ribosomal protein L30 NA BCG_0773 1.17 Rv0723 rplO 50S ribosomal protein L15 10 BCG_1025c 1.22 2.25 Rv0971c echA7 enoyl-CoA hydratase BCG_1026c 1.64 2.74 Rv0972c fadE12...”
• HflX is a GTPase that controls hypoxia-induced replication arrest in slow-growing mycobacteria
  Ngan, Proceedings of the National Academy of Sciences of the United States of America 2021 (secret)
• Biosafety and Proteome Profiles of Different Heat Inactivation Methods for Mycobacterium tuberculosis
  Wang, Microbiology spectrum 2021
  • “...serine protease HtrA1 6 6 6 17 37 4,271,000 2,615,200 5,256,267 0.61 1.23 2.01 sp| P9WHA3 |RL30_MYCTU 50S ribosomal protein L30 2 2 2 43 105 8,095,500 14,713,333 16,803,567 1.82 2.08 1.14 sp| P9WJV5 |MMPL3_MYCTU Trehalose monomycolate exporter MmpL3 8 8 8 14 77 6,792,050 2,879,250...”
• 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, MT0062...”
• Metabolic Changes of Mycobacterium tuberculosis during the Anti-Tuberculosis Therapy
  Bespyatykh, Pathogens (Basel, Switzerland) 2020
  • “...that in 2093 samples, abundance of RpsL and seven other ribosome proteins (Rv0055, Rv0714, Rv0720, Rv0722, Rv0979A, Rv1298, and Rv2412) was lower compared to the parental strains. This finding may be related to the fact that ribosomal proteins can be targeted by anti-tuberculosis drugs [ 16...”
• Role of VapBC12 Toxin-Antitoxin Locus in Cholesterol-Induced Mycobacterial Persistence
  Talwar, mSystems 2020
  • “...Rv3078 ( hab ) Up 7.058740267 Intermediary metabolism and respiration Rv1505c Up 8.135570656 Conserved hypotheticals Rv0722 ( rpmD ) Up 5.031834752 Information pathways Rv0129c ( fbpC ) Up 1.398249199 Lipid metabolism Rv1909c ( furA ) Down 3.361374217 Regulatory proteins Rv1183 ( mmpL10 ) Up 1.272401462 Cell...”
  • “...Information pathways 60 Rv2058c Information pathways 66.66666667 Rv2056c Information pathways 66.66666667 Rv1643 Information pathways 66.66666667 Rv0722 Information pathways 100 Rv2441c Information pathways 100 Rv3053c Information pathways 100 Rv3462c Information pathways 100 Rv1772 Conserved hypotheticals 60 Rv0678 Conserved hypotheticals 60 Rv0607 Conserved hypotheticals 60 Rv3678A Conserved hypotheticals...”
• The effect of growth rate on pyrazinamide activity in Mycobacterium tuberculosis - insights for early bactericidal activity?
  Pullan, BMC infectious diseases 2016
  • “...P95057 50S ribosomal protein L29 4.32 4.82 Rv0702 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...”
  • “...P95051 50S ribosomal protein L23 1.60 2.33 Rv0700 P0A5X0 30S ribosomal protein S10 1.51 2.40 Rv0722 P66181 50S ribosomal protein L30 1.14 2.42 tRNA-Val tRNA-Val 1.79 2.45 Rv0709 P95057 50S ribosomal protein L29 1.90 2.72 Rv0710 P95058 30S ribosomal protein S17 1.10 2.04 tRNA-Met tRNA-Met Genes...”
• InbR, a TetR family regulator, binds with isoniazid and influences multidrug resistance in Mycobacterium bovis BCG
  Yang, Scientific reports 2015
  • “...L29 Up BCG_0760 1.79 1.94 Rv0710 rpsQ 30S ribosomal protein S17 9 BCG_0772 1.64 1.52 Rv0722 rpmD 50S ribosomal protein L30 NA BCG_0773 1.17 Rv0723 rplO 50S ribosomal protein L15 10 BCG_1025c 1.22 2.25 Rv0971c echA7 enoyl-CoA hydratase BCG_1026c 1.64 2.74 Rv0972c fadE12 acyl-CoA dehydrogenase fadE12...”
• Mycobacterium tuberculosis septum site determining protein, Ssd encoded by rv3660c, promotes filamentation and elicits an alternative metabolic and dormancy stress response
  England, BMC microbiology 2011
  • “...rplC -1.5 -0.4 Rv3550 echA20 1.1 0.2 Rv0716 rplE -1.2 -0.9 Rv0971c echA7 1.3 -0.1 Rv0722 rpmD -0.9 -0.3 Rv3546 fadA5 1.1 0.1 Rv0723 rplO -0.7 -0.2 Rv1715 fadB3 1.0 -0.1 Rv2441c rpmA -0.9 -0.5 Rv0099 fadD10 1.2 0.0 Rv3442c rpsI -0.9 -0.2 Rv1550 fadD11 1.0...”
• Sequence-based analysis uncovers an abundance of non-coding RNA in the total transcriptome of Mycobacterium tuberculosis
  Arnvig, PLoS pathogens 2011
  • “...gene class RPKM Rv0009 ppiA II.A.6 878 Rv3418c groES III.B 814 Rv3874 esxB VI 594 Rv0722 rpmD II.A.1 581 Rv3460c rpsM II.A.1 538 Rv3477 PE31 IV.C.1 521 Rv1872c lldD2 I.B.6a 497 Rv3408 vapC hom V 482 Rv0685 tuf II.A.6 479 Rv1305 atpE I.B.8 456 Rv3462c infA...”
• Mycobacterium tuberculosis modulates its cell surface via an oligopeptide permease (Opp) transport system
  Flores-Valdez, FASEB journal : official publication of the Federation of American Societies for Experimental Biology 2009
  • “...Rv0651 Rv0693 Rv0700 Rv0702 Rv0704 Rv0706 Rv0708 Rv0710 Rv0714 Rv0716 Rv0722 Rv0859 Rv0860 Rv0878c Rv0963c 1.3 1.6 1.1 1.3 1.1 1.4 1.1 1.1 1.2 1.2 1.1 1.1 1.1...”
• Rv2629 Overexpression Delays Mycobacterium smegmatis and Mycobacteria tuberculosis Entry into Log-Phase and Increases Pathogenicity of Mycobacterium smegmatis in Mice
  Liu, Frontiers in microbiology 2017
  • “...YP_001282298.1 Molybdopterin biosynthesis protein MoeA1 Up Up Up MRA_0827 YP_001282118.1 Hypothetical protein Up Up Up MRA_0730 YP_001282020.1 50S ribosomal protein L30 Up Up Up MRA_0716 YP_001282006.1 50S ribosomal protein L16 Up Up Up MRA_0639 YP_001281925.1 Exodeoxyribonuclease V subunit beta Up Up Up MRA_0619 YP_001281905.1 Hypothetical protein...”

RL30_THET8 / Q5SHQ6 Large ribosomal subunit protein uL30; 50S ribosomal protein L30 from Thermus thermophilus (strain ATCC 27634 / DSM 579 / HB8) (see paper)
6b4vAA / Q72I22 blasticidin S and E. coli release factor 1 bound to the 70S ribosome (see paper)
TTC1310 No description from Thermus thermophilus HB27
46% identity, 95% coverage

• subunit: Part of the 50S ribosomal subunit
• Ligand: rna (6b4vAA)
• Comparative genomics of Thermus thermophilus and Deinococcus radiodurans: divergent routes of adaptation to thermophily and radiation resistance
  Omelchenko, BMC evolutionary biology 2005
  • “...Proteobacterial affinity of DR; Affinity to Thermatoga/Aquifex/other Gram-positive bacteria in TT Ribosomal protein L30/L7E (COG1841) TTC1310 DR2114 Thermatogales/Aquifecales version in TT, affinity to other bacteria in DR Thiamine biosynthesis protein ThiC (COG0422) TTC0319 DRA0175 Proteobacterial affinity in DR; Cyanobacteria/Actinobacterial affinity in TT Threonine synthase (COG0498) TTC0117...”

PGN_1850 50S ribosomal protein L30 from Porphyromonas gingivalis ATCC 33277
52% identity, 98% coverage

• Pathway analysis for intracellular Porphyromonas gingivalis using a strain ATCC 33277 specific database
  Hendrickson, BMC microbiology 2009
  • “...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 internalized P. gingivalis versus external control...”

lpg0347 50S ribosomal protein L30/(L7E) from Legionella pneumophila subsp. pneumophila str. Philadelphia 1
46% identity, 93% coverage

• Legionella Pneumophila Transcriptome during Intracellular Multiplication in Human Macrophages
  Faucher, Frontiers in microbiology 2011
  • “...family transporter lbtB 3.1 3.9 5.4 5.2 lpg1420 Cytidylate kinase cmk 2.3 2.1 2.5 2.8 lpg0347 50S ribosomal protein L30/(L7E) rpmD 2.9 2.0 2.6 2.9 lpg2292 tRNA-Gly 1.6 2.8 2.7 3.0 lpg2752 tRNA-Ile 0.7 2.8 3.4 3.2 lpg2902 Conserved hypothetical protein 0.8 3.5 3.2 3.3 lpg0303...”

D0R1L5 Large ribosomal subunit protein uL30 from Lactobacillus johnsonii (strain FI9785)
53% identity, 92% coverage

• Identification of Genes Required for Glucan Exopolysaccharide Production in Lactobacillus johnsonii Suggests a Novel Biosynthesis Mechanism
  Mayer, Applied and environmental microbiology 2020
  • “...X tRNA processing; tRNA 3-trailer cleavage, endonucleolytic; tRNA 3-trailer cleavage; RNA phosphodiester bond hydrolysis, endonucleolytic D0R1L5 50S ribosomal protein L30 rpmD 2 6 37 1.81 0.29 3.50 X X Translation D0R1U3 Tryptophan-tRNA ligase trpS 8 39 269 1.80 0.29 3.47 X Translation; tRNA aminoacylation for protein...”

7f0dZ / A5U0A8 Cryo-em structure of mycobacterium tuberculosis 50s ribosome subunit bound with clarithromycin (see paper)
50% identity, 95% coverage

• Ligand: rna (7f0dZ)

MAP4185 RpmD from Mycobacterium avium subsp. paratuberculosis str. k10
50% identity, 79% coverage

• Proteome and differential expression analysis of membrane and cytosolic proteins from Mycobacterium avium subsp. paratuberculosis strains K-10 and 187
  Radosevich, Journal of bacteriology 2007
  • “...41395961 gi 41396190 gi 41398220 MAP1589c MAP0961c MAP4185 MAP1826c MAP2120c MAP2987c MAP2793 MAP3396c MAP0962c MAP1316c MAP4183 MAP3717c MAP1042 MAP0631c...”

7jilZ / A0A1M5L7Z6 7jilZ (see paper)
54% identity, 95% coverage

• Ligand: rna (7jilZ)

EAMY_3368 50S ribosomal protein L30 from Erwinia amylovora CFBP1430
47% identity, 98% coverage

• The stringent response regulator (p) ppGpp mediates virulence gene expression and survival in Erwinia amylovora
  Yang, BMC genomics 2020
  • “...rpmE , ribosomal protein L31 2.64 9.97 EAMY_0078 rpmG , ribosomal protein L33 2.43 10.07 EAMY_3368 rpmD , ribosomal protein L30 1.8 10.52 EAMY_0077 rpmB , ribosomal protein L28 1.76 10.47 EAMY_0333 rpmA , ribosomal protein L27 1.64 11.06 rps EAMY_0304 rpsI , ribosomal protein S9...”

RpmD / b3302 50S ribosomal subunit protein L30 from Escherichia coli K-12 substr. MG1655 (see 5 papers)
rpmD / P0AG51 50S ribosomal subunit protein L30 from Escherichia coli (strain K12) (see 2 papers)
RL30_ECOLI / P0AG51 Large ribosomal subunit protein uL30; 50S ribosomal protein L30 from Escherichia coli (strain K12) (see 9 papers)
ECs4167 50S ribosomal subunit protein L30 from Escherichia coli O157:H7 str. Sakai
NP_417761 50S ribosomal subunit protein L30 from Escherichia coli str. K-12 substr. MG1655
b3302 50S ribosomal protein L30 from Escherichia coli str. K-12 substr. MG1655
NP_709090 50S ribosomal subunit protein L30 from Shigella flexneri 2a str. 301
51% identity, 98% coverage

• subunit: Part of the 50S ribosomal subunit.
• Global transcriptional response of Escherichia coli O157:H7 to growth transitions in glucose minimal medium
  Bergholz, BMC microbiology 2007
  • “...rpsM -3.05 1 ECs4463 yiaW 2.75 2 ECs4166 rplO -3.63 1 ECs4464 aldB 3.02 2 ECs4167 rpmD -3.70 1 ECs4473 yibH 3.78 2 ECs4168 rpsE -3.75 1 ECs4475 mtlA 2.84 2 ECs4169 rplR -3.75 1 ECs4511 rpmG -3.21 1 ECs4170 rplF -3.62 1 ECs4514 dfp -2.28...”
• The primary structure of protein L30 from Escherichia coli ribosomes.
  Ritter, FEBS letters 1975 (PubMed)
  • GeneRIF: N-terminus verified by Edman degradation on mature peptide
• Liquid-Liquid Phase Separation and Protective Protein Aggregates in Bacteria
  Kuczyńska-Wiśnik, Molecules (Basel, Switzerland) 2023
  • “...emPAI %). ID Protein Names emPAI % Abundance PaxDb (ppm) catGranule FuzDrop pLLPS PSPredictor 1 P0AG51 50S ribosomal protein L30 2.88 6056 0.970 0.117 0.005 2 P02413 50S ribosomal protein L15 2.82 3541 2.075 0.514 0.285 3 P62399 50S ribosomal protein L5 2.79 5965 0.283 0.114...”
• Capturing Membrane Protein Ribosome Nascent Chain Complexes in a Native-like Environment for Co-translational Studies
  Pellowe, Biochemistry 2020
  • “...RL22, P61175; RL23, P0ADZ0; RL24, P60624; RL25, P68919; RL27, P0A7M0; RL28, P0A7M2; RL29, P0A7M6; RL30, P0AG51; RL31, P0A7M9; RL32, C4ZS29; RL33, P0A7N9; RL34, P0A7P6; RL35, P0A7Q2; RL36, P0A7Q7. Author Contributions G.A.P., E.R., and P.J.B. designed the research. G.A.P., H.E.F., K.L., T.M.G., and E.R. performed all experiments...”
• Stress response of Escherichia coli to essential oil components - insights on low-molecular-weight proteins from MALDI-TOF
  Božik, Scientific reports 2018
  • “...and, to a lesser extent, exponential phase 72 . 50S ribosomal protein L30 (m/z 6411,04, P0AG51, rpmD) was highly induced by thymol, carvacrol and cinnamaldehyde. This protein is structural constituent of the ribosome and functions in the aggregation, arrangement and bonding of constituent RNAs and proteins...”
• Analysis of promoter targets for Escherichia coli transcription elongation factor GreA in vivo and in vitro
  Stepanova, Journal of bacteriology 2007
  • “...rpsE rplR rplF rpsH rpsN rplE rplX rplN b3299 b3300 b3301 b3302 b3303 b3304 b3305 b3306 b3307 b3308 b3309 b3310 2.7 4.3 3.1 3.7 3.7 3.1 4.1 3.2 3.2 2.7 3.2 3.3...”
• Interfering with different steps of protein synthesis explored by transcriptional profiling of Escherichia coli K-12
  Sabina, Journal of bacteriology 2003
  • “...b0642 b3460 b3829 b4143 b0957 b3315 b3302 b3342 b0146 b4062 b2607 b1262 b3781 b1004 GCCAAAACACTGGAACTGGT CGGCAAATAAAACCCTGTTG CATTGAGCCTGCAACAAGAA...”
  • “...b0696 b4017 b0188 b2578 b1749 b3242 b3104 b1736 b3299 b0011 b1447 b3302 b1451 b2261 b0285 b1600 b0174 b2534 b0154 b3312 b1400 82 77 59 28 27 24 24 20 19 17 16...”
• Microarray analysis of orthologous genes: conservation of the translational machinery across species at the sequence and expression level
  Jiménez, Genome biology 2003
  • “...secretion Ribosomal protein 11 b3301 Yes** COG0200 J4 50S ribosomal protein L15 Ribosomal protein 11 b3302 Yes** COG1841 J4 50S ribosomal protein L30 Ribosomal protein 11 b3303 Yes** COG0098 J3 30S ribosomal protein S5 Ribosomal protein 11 b3304 Yes** COG0256 J4 50S ribosomal protein L18 Ribosomal...”
• Combined, functional genomic-biochemical approach to intermediary metabolism: interaction of acivicin, a glutamine amidotransferase inhibitor, with Escherichia coli K-12
  Smulski, Journal of bacteriology 2001
  • “...yjjR yjjS yjjT zwf b3318 b3309 b2185 b3185 b3637 b3302 b3636 b3703 b3299 b3295 b3314 b3296 b3303 b4200 b3341 b3306 b3230 b3321 b3297 b3298 b3307 b2609 b3311...”
• Genome-wide transcriptional profiling of the Escherichia coli responses to superoxide stress and sodium salicylate
  Pomposiello, Journal of bacteriology 2001
  • “...b3294 b3304 b3186 b3315 b3318 b3309 b3185 b3637 b3312 b3302 b1717 b3299 b3295 b0169 b3314 b3296 b3303 b3306 b3230 b3321 b3297 b3307 b2609 b3311 atpA atpC atpF...”
• Computational Identification of Essential Enzymes as Potential Drug Targets in Shigella flexneri Pathogenesis Using Metabolic Pathway Analysis and Epitope Mapping
  Narad, Journal of microbiology and biotechnology 2021
  • “...protein L28 Cytoplasm No Hits 15 NP_709100 50S ribosomal protein L29 Cytoplasm No Hits 16 NP_709090 50S ribosomal protein L30 Cytoplasm No Hits 17 NP_709740 50S ribosomal protein L31 Cytoplasm No Hits 18 NP_707005 50S ribosomal protein L32 Cytoplasm No Hits 19 NP_709497 50S ribosomal protein...”

8a3ly / P0AG51 8a3ly (see paper)
49% identity, 93% coverage

• Ligand: rna (8a3ly)

Q88XW8 Large ribosomal subunit protein uL30 from Lactiplantibacillus plantarum (strain ATCC BAA-793 / NCIMB 8826 / WCFS1)
49% identity, 95% coverage

• Proteomic Analysis Explores Interactions between Lactiplantibacillus plantarum and Saccharomyces cerevisiae during Sourdough Fermentation
  Zhang, Microorganisms 2021
  • “...Ribosomal Protein S8 up - - - A0A199QKN2 Ribosomal Protein L6 up - - - Q88XW8 Ribosomal Protein L30 up - - - W5BFB7 Ribosomal Protein S11 up - - - W5E6W1 Ribosomal Protein L23 - - up up P41057 Ribosomal Protein S29 - up -...”

9c4gy / A0A2B7I5Y4 Cutibacterium acnes 50s ribosomal subunit with clindamycin bound (see paper)
45% identity, 98% coverage

• Ligand: rna (9c4gy)

SPA3288 50S ribosomal subunit protein L30 from Salmonella enterica subsp. enterica serovar Paratyphi A str. ATCC 9150
B5R1F9 Large ribosomal subunit protein uL30 from Salmonella enteritidis PT4 (strain P125109)
P0A2A7 Large ribosomal subunit protein uL30 from Salmonella typhimurium (strain LT2 / SGSC1412 / ATCC 700720)
STM3422 50S ribosomal subunit protein L30 from Salmonella typhimurium LT2
SEN3250 50S ribosomal subunit protein L30 from Salmonella enterica subsp. enterica serovar Enteritidis str. P125109
SENTW_3549 50S ribosomal protein L30 from Citrobacter braakii
47% identity, 98% coverage

• Analysis of Salmonella enterica serotype paratyphi A gene expression in the blood of bacteremic patients in Bangladesh
  Sheikh, PLoS neglected tropical diseases 2010
  • “...3.09 0.0203 SPA3012 hybF Hydrogenase-2 component protein 5.51 0.0028 6.58 0.0281 5.56 0.0212 Protein synthesis SPA3288 rpmD 50S ribosomal subunit protein L30 7.81 0.0029 4.42 0.0275 3.47 0.0217 SPA3289 rpsE 30S ribosomal subunit protein S5 7.16 0.0042 4.19 0.0276 4.03 0.0196 SPA3290 rplR 50S ribosomal subunit...”
• Ethanol Adaptation Strategies in Salmonella enterica Serovar Enteritidis Revealed by Global Proteomic and Mutagenic Analyses
  He, Applied and environmental microbiology 2019 (secret)
• N-dodecanoyl-homoserine lactone influences the levels of thiol and proteins related to oxidation-reduction process in Salmonella
  de, PloS one 2018
  • “...Translation -1.525 1.640 8.702 1.677 1.191 0.481 -0.900 2.043 0.539 0.280 50S ribosomal protein L30 P0A2A7 rpmD Translation ND ND ND ND ND ND ND ND -9.619 2.532 50S ribosomal protein L31 P66191 rpmE Translation ND ND ND ND ND ND 10.159 1.074 ND ND 50S...”
• 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
  • “...INTESTINE 4111 TABLE 3--Continued COGs class Gene STM3430 STM3422 STM4393 STM3441 STM0981 STM3447 STM3448 STM3436 STM3419 STM1335 rplN rplP rpsR rpsJ rpsA rpsG...”
• Global transcriptomic analysis of ethanol tolerance response in Salmonella Enteritidis
  He, Current research in food science 2022
  • “...S20 SEN3935 rplJ 3.32 50S ribosomal protein L10 SEN2594 rplS 3.71 50S ribosomal protein L19 SEN3250 rpmD 4.40 50S ribosomal protein L30 SEN1708 rplT 2.80 50S ribosomal protein L20 SEN0223 rpsB 2.97 30S ribosomal protein S2 SEN3242 rplQ 4.30 50S ribosomal protein L17 SEN3262 rpsC 3.69...”
• Transcriptional profile of Salmonella enterica subsp. enterica serovar Weltevreden during alfalfa sprout colonization
  Brankatschk, Microbial biotechnology 2014
  • “...rpmA SENTW_3431 6.60 50S ribosomal protein L27 rpmB SENTW_3829 5.06 50S ribosomal protein L28 rpmD SENTW_3549 3.82 50S ribosomal protein L30 rpmF SENTW_2062 6.82 50S ribosomal protein L32 rpmG SENTW_3828 8.15 50S ribosomal protein L33 rpmJ SENTW_3546 5.27 50S ribosomal subunit protein L36 rpsH SENTW_3553 10.11...”

bglu_1g02760 50S ribosomal protein L30 from Burkholderia glumae BGR1
49% identity, 84% coverage

• RNAseq-based Transcriptome Analysis of Burkholderia glumae Quorum Sensing
  Kim, The plant pathology journal 2013
  • “...0.9 1.4 1.5 bglu_1g02740 rplR 1.3 0.8 1.3 1.5 bglu_1g02750 rpsE 1.2 0.8 1.2 1.2 bglu_1g02760 rpm 1.3 0.7 1. 1 bglu_1g02770 rplO 1.2 0.6 1.3 1.3 bglu_1g02800 rpmJ 1.3 1 1.3 1.4 bglu_1g02810 rpsM 1.1 0.7 1.4 1.4 bglu_1g02820 rpsK 1.1 0.8 1.3 1.2 bglu_1g02830...”

BB562_12015 50S ribosomal protein L30 from Lactiplantibacillus pentosus
47% identity, 95% coverage

• Transcriptomic Profile and Probiotic Properties of Lactiplantibacillus pentosus Pre-adapted to Edible Oils
  Alonso, Frontiers in microbiology 2021
  • “...glycerol-3-phosphate ABC transporter permease (ABC transporters), down-regulation of two additional genes coding for ribosome proteins (BB562_12015 and BB562_11990; Supplementary Table 2 and Supplementary Figure 3 ), and encoding serine acetyltransferase (BB562_01130) involved in sulfur metabolism ( Supplementary Table 2 and Supplementary Figure 3 ). Other new...”

RL30_DEIRA / Q9RSL0 Large ribosomal subunit protein uL30; 50S ribosomal protein L30 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)
7a0rW / Q9RSL0 50s deinococcus radiodurans ribosome bounded with mycinamicin i (see paper)
DR2114 ribosomal protein L30 from Deinococcus radiodurans R1
47% identity, 93% coverage

• function: Binds the 5S and 23S rRNAs
  subunit: Part of the 50S ribosomal subunit.
• Ligand: rna (7a0rW)
• Comparative genomics of Thermus thermophilus and Deinococcus radiodurans: divergent routes of adaptation to thermophily and radiation resistance
  Omelchenko, BMC evolutionary biology 2005
  • “...affinity of DR; Affinity to Thermatoga/Aquifex/other Gram-positive bacteria in TT Ribosomal protein L30/L7E (COG1841) TTC1310 DR2114 Thermatogales/Aquifecales version in TT, affinity to other bacteria in DR Thiamine biosynthesis protein ThiC (COG0422) TTC0319 DRA0175 Proteobacterial affinity in DR; Cyanobacteria/Actinobacterial affinity in TT Threonine synthase (COG0498) TTC0117 DRA0360...”

GSU2839 ribosomal protein L30 from Geobacter sulfurreducens PCA
49% identity, 97% coverage

• Role of RelGsu in stress response and Fe(III) reduction in Geobacter sulfurreducens
  DiDonato, Journal of bacteriology 2006
  • “...RT_ORF04677_F RT_ORF04677_R AAGCTCGGCACTCAGATGAT GCTTGTGCTCGGGAGAATAC GSU2839 Ribosomal protein L30 RT_ORF04707_F RT_ORF04707_R ATATCGGGACGACCAGCAAG...”
  • “...Fold changea Gene category Locus Annotation qRT-PCR GSU2409 GSU2839 GSU2875 GSU1346 Heat shock protein, Hsp20 family Ribosomal protein L30 Ribosomal protein S9...”

AL022_RS00600 50S ribosomal protein L30 from Cardinium endosymbiont cEper1 of Encarsia pergandiella
46% identity, 92% coverage

• Transcriptome Sequencing Reveals Novel Candidate Genes for Cardinium hertigii-Caused Cytoplasmic Incompatibility and Host-Cell Interaction
  Mann, mSystems 2017
  • “...3,335.95 0.90 <0.001 0.009 AL022_RS02585 CAHE_0565 Transcription elongation factor GreA 141.55 264.19 0.90 0.001 0.052 AL022_RS00600 CAHE_0130 50S ribosomal protein L30 147.84 274.74 0.89 <0.001 0.052 AL022_RS01110 Aspartate-tRNA ligase 214.87 390.65 0.86 <0.001 0.040 AL022_RS01125 CAHE_0242 Dipeptide transport system permease protein OppC 212.17 384.43 0.86 <0.001...”

AS87_07825 50S ribosomal protein L30 from Riemerella anatipestifer Yb2
45% identity, 98% coverage

• Deletion of AS87_03730 gene changed the bacterial virulence and gene expression of Riemerella anatipestifer
  Wang, Scientific reports 2016
  • “...AS87_02865 hypothetical protein Cytoplasmic 1.75 AS87_04500 hypothetical protein Unknown 1.72 AS87_07455 membrane protein Unknown 1.65 AS87_07825 50S ribosomal protein L30 Cytoplasmic COG1841 J 1.65 AS87_07870 50S ribosomal protein L17 Cytoplasmic COG0203 J 1.57 AS87_01795 membrane-binding protein Unknown 1.55 AS87_05160 30S ribosomal protein S10 Cytoplasmic COG0051 J...”

HMPREF0424_0269 ribosomal protein L30 from Gardnerella vaginalis 409-05
47% identity, 97% coverage

• Comparative transcriptomic analysis of Gardnerella vaginalis biofilms vs. planktonic cultures using RNA-seq
  Castro, NPJ biofilms and microbiomes 2017
  • “...Fold-change (Biofilm vs. planktonic cells) Rank Downregulated 1 HMPREF0424_0046 50S ribosomal protein L34 21.93 2 HMPREF0424_0269 50S ribosomal protein L30 8.99 3 HMPREF0424_0429 (xseA) Exodeoxyribonuclease VII large subunit 6.73 4 HMPREF0424_0260 30S ribosomal protein S3 5.43 5 HMPREF0424_1336 Periplasmic-binding protein and sugar-binding domain of the LacI...”

TP0206a ribosomal protein L30 from Treponema pallidum subsp. pallidum str. Nichols
48% identity, 92% coverage

• Characterizing the Syphilis-Causing Treponema pallidum ssp. pallidum Proteome Using Complementary Mass Spectrometry
  Osbak, PLoS neglected tropical diseases 2016
  • “...N TP1012 O83976 RNA polymerase sigma factor 35 7.4 0.5 DNA-templated transcription; initiation Polymerase K TP0206a R9UU00 50S ribosomal protein L30 7 7.4 2.0 Translation Ribosome no_hit TP0194 R9UVW4 50S ribosomal protein L22 14 7.3 1.8 Translation Ribosome J TP0234 R9UU20 50S ribosomal protein L33 7...”
• Whole genome sequences of three Treponema pallidum ssp. pertenue strains: yaws and syphilis treponemes differ in less than 0.2% of the genome sequence
  Cejková, PLoS neglected tropical diseases 2012
  • “...the previously published TPA Nichols genome sequence (AE000520, [23] ), the orthologs of TPE genes TP0206a, TP0451a, TP0949a, and TP0950a were later annotated in the Nichols genome (GenBank AE000520.1). These genes are therefore not listed in Table S1 , which lists only newly annotated genes. Moreover,...”

7pktx / A0A2K3DSP9 7pktx (see paper)
43% identity, 32% coverage

• Ligand: rna (7pktx)

FN1626 LSU ribosomal protein L30P from Fusobacterium nucleatum subsp. nucleatum ATCC 25586
41% identity, 95% coverage

• Proteomics of Fusobacterium nucleatum within a model developing oral microbial community
  Hendrickson, MicrobiologyOpen 2014
  • “...FN0482, FN1117, FN1119, FN1282, FN1284, FN1285, FN1286, FN1364, FN1392, FN1437, FN1557, FN1558, FN1620, FN1623, FN1625, FN1626, FN1627, 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...”

SPO0503 50S ribosomal protein L30 from Ruegeria pomeroyi DSS-3
49% identity, 79% coverage

• A mutant fitness assay identifies bacterial interactions in a model ocean hot spot
  Schreier, Proceedings of the National Academy of Sciences of the United States of America 2023
  • “...Cell cycle/growth 0.11 SPO_Sp16SB 16S rRNA Cell cycle/growth 0.13 SPO_Sp16SC 16S rRNA Cell cycle/growth 0.14 SPO0503 ribosomal protein L30 ( rpmD) Cell cycle/growth 0.34 SPO1443 ATP-dependent RNA helicase RhlE ( rhlE ) Cell cycle/growth 0.44 0.36 0.42 SPO3256 ribosomal protein L31 ( rpmE ) Cell cycle/growth...”

A1JS10 Large ribosomal subunit protein uL30 from Yersinia enterocolitica serotype O:8 / biotype 1B (strain NCTC 13174 / 8081)
44% identity, 98% coverage

• Deconvolution and database search of complex tandem mass spectra of intact proteins: a combinatorial approach
  Liu, Molecular & cellular proteomics : MCP 2010
  • “...14,988.35 Da 13 8 11 8 9 8 11 13 A1JHR2 A1JN60 A1JQX1a A1JS10 A1JS26 A1JK11 A1JS31 A1JIS8 65 57 32 93 92 31 31 31 131 131 131 131 NME NME NME NME AIJQX1 is not...”

B2B147 Large ribosomal subunit protein uL30m from Podospora anserina (strain S / ATCC MYA-4624 / DSM 980 / FGSC 10383)
47% identity, 46% coverage

• CLPP-Null Eukaryotes with Excess Heme Biosynthesis Show Reduced L-arginine Levels, Probably via CLPX-Mediated OAT Activation
  Key, Biomolecules 2024
  • “...(SAM)-dependent O-methyltransferase (B2ADP0, homologous to yeast Tae1), homologs of the mitoribosomal large subunit proteins uL30m (B2B147, ferredoxin-like) and bL33 (B2ARQ6, zinc-binding), and a heterokaryon incompatibility protein (B2AMZ4). The dysregulation of SAM-dependent methyltransferases is substantiated further by the significant upregulation of B2B823 and B2AQK9 ( Figure 4...”
  • “...]. In the P. anserina CLPP-null proteome profile, two LSU proteins showed a massive upregulation. B2B147 has a ferredoxin-like -----fold core structure, and B2ARQ6 has a zinc-binding domain, so both factors potentially associate with heavy metals, and recent mouse analyses documented several heavy metals accumulating in...”

H375_8910 50S ribosomal protein L30 from Rickettsia prowazekii str. Breinl
43% identity, 84% coverage

• Transcriptional profiling of Rickettsia prowazekii coding and non-coding transcripts during in vitro host-pathogen and vector-pathogen interactions
  Schroeder, Ticks and tick-borne diseases 2017
  • “...guanosine-3,5-bis(diphosphate) 3-pyrophosphohydrolase SpoTc H375_2110 12.26 Signal peptide peptidase SppA, 36K type H375_0670 11.93 Citrate synthase H375_8910 11.77 LSU ribosomal protein L30p H375_1070 10.94 Lipopolysaccharide-assembly protein LptC H375_0860 10.77 Fumarate hydratase class II H375_5480 10.27 hypothetical protein H375_7110 9.69 YrbA protein H375_1170 9.61 Multicopper polyphenol oxidase H375_0490...”

HI0796 ribosomal protein L30 (rpL30) from Haemophilus influenzae Rd KW20
46% identity, 98% coverage

• Initial proteome analysis of model microorganism Haemophilus influenzae strain Rd KW20
  Kolker, Journal of bacteriology 2003
  • “...HI1320 HI0880 HI0782 HI0779 HI0789 HI1630 HI0879 HI0951 HI0785 HI0796 HI0758 HI0158 HI0950 HI0998 HI1319m HI0798.1 550 252 236 207 167 131 157 131 131 119 130...”

SO0249 ribosomal protein L30 from Shewanella oneidensis MR-1
42% identity, 92% coverage

• Transcriptome analysis reveals a stress response of Shewanella oneidensis deprived of background levels of ionizing radiation
  Castillo, PloS one 2018
  • “...protein S14 -1.09 SO0247 rplR Ribosomal protein L18 -1.20 SO0248 rpsE Ribosomal protein S5 -1.04 SO0249 rpmD Ribosomal protein L30 -1.13 SO0250 rplO Ribosomal protein L15 -1.15 SO0252 rpmJ Ribosomal protein L36 -1.01 -1.07 SO0253 rpsM Ribosomal protein S13 -1.02 SO0257 rplQ Ribosomal protein L17p -1.04...”
• Global molecular and morphological effects of 24-hour chromium(VI) exposure on Shewanella oneidensis MR-1
  Chourey, Applied and environmental microbiology 2006
  • “...SO0231 to SO0240, SO0243, SO0244, and SO0246 to SO0249). The membrane response was characterized by changes in the expression of genes encoding outer membrane...”

RM33_NEUCR / Q1K8Y7 Large ribosomal subunit protein uL30m from Neurospora crassa (strain ATCC 24698 / 74-OR23-1A / CBS 708.71 / DSM 1257 / FGSC 987) (see 2 papers)
43% identity, 36% 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.

NMA0111 50S ribosomal protein L30 from Neisseria meningitidis Z2491
NMB0160 50S ribosomal protein L30 from Neisseria meningitidis MC58
44% identity, 90% coverage

• Transcriptome analysis of Neisseria meningitidis during infection
  Dietrich, Journal of bacteriology 2003
  • “...NMA0128 NMA0127 NMA0123 NMA0122 NMA0121 NMA0120 NMA0112 NMA0111 NMA0110 NMA0108 NMA0107 NMA0104 NMA0102 NMA1137 NMA1138 NMA0027 NMA1303/NMA1188 Absent Absent...”
• Transcriptome analysis of Neisseria meningitidis during infection
  Dietrich, Journal of bacteriology 2003
  • “...NMB0143 NMB0144 NMB0148 NMB0149 NMB0150 NMB0151 NMB0159 NMB0160 NMB0161 NMB0163 NMB0164 NMB0167 NMB0169 NMB0941 NMB0942 NMB0232 NMB0987 NMB0961 NMB0091 NMB0092...”

PA4245 50S ribosomal protein L30 from Pseudomonas aeruginosa PAO1
PA14_09030 50S ribosomal protein L30 from Pseudomonas aeruginosa UCBPP-PA14
40% identity, 97% coverage

• Distinct transcriptome and traits of freshly dispersed <i>Pseudomonas aeruginosa</i> cells
  Kalia, mSphere 2024
  • “...ATPase Upregulated 1.274297 Upregulated 1.608189 PA4239 Upregulated 1.027846 Upregulated 0.613988 PA4244 Upregulated 1.057922 Upregulated 0.741539 PA4245 rpmD-50S ribosomal protein L30 Upregulated 1.083746 Upregulated 0.966522 PA4248 Upregulated 1.036283 Upregulated 0.702379 PA4249 rpsH-30S ribosomal protein S8 Upregulated 1.439878 Upregulated 1.194785 PA4255 rpmC-50S ribosomal protein L29 Upregulated 0.987271 Upregulated...”
• Reverse diauxie phenotype in Pseudomonas aeruginosa biofilm revealed by exometabolomics and label-free proteomics
  Yung, NPJ biofilms and microbiomes 2019
  • “...NR NR NR NR RplT PA2741 50S ribosomal protein L20 NR NR NR NR RpmD PA4245 50S ribosomal protein L30 NR NR NR NR NR RpmE PA5049 50S ribosomal protein L31 NR NR NR NR NR RpsL PA4268 30S ribosomal protein S12 NR NR NR NR...”
• Analysis of Pseudomonas aeruginosa cell envelope proteome by capture of surface-exposed proteins on activated magnetic nanoparticles
  Vecchietti, PloS one 2012
  • “...rpsQ PA4254 30S rP S17 2 C,3 rplB PA4260 50S rP L2 2 C,3 rpmD PA4245 50S rP L30 2 C,3 rplS PA3742 50S rP L19 2 C,3 rpmF PA2970 50S rP L32 2 C,3 rluB PA3179 Putative ribosomal pseudouridine synthase B 4 C,3 a Class...”
• 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
  • “...PA4053 PA4220 PA4238 PA4239 PA4240 PA4241 PA4242 PA4243 PA4245 PA4246 PA4247 PA4248 PA4249 PA4252 PA4254 PA4257 PA4258 PA4259 PA4260 PA4261 PA4262 PA4263 PA4266...”
• Loss of the Two-Component System TctD-TctE in Pseudomonas aeruginosa Affects Biofilm Formation and Aminoglycoside Susceptibility in Response to Citric Acid
  Taylor, mSphere 2019
  • “...2.12 PA14_21760 capB Cold acclimation protein B 2.13 PA14_65160 2.14 PA14_14440 valS Valyl-tRNA synthetase 2.15 PA14_09030 rpmD 50S ribosomal protein L30 2.15 PA14_66230 waaG UDP-glucose:(heptosyl) LPS alpha 1,3-glucosyltransferase 2.15 PA14_17675 dgkA Diacylglycerol kinase 2.16 PA14_09050 secY Secretion protein SecY 2.18 PA14_70640 rubA1 Rubredoxin 1 2.20 PA14_73420...”

AT5G55140 ribosomal protein L30 family protein from Arabidopsis thaliana
39% identity, 51% coverage

• An Update on Mitochondrial Ribosome Biology: The Plant Mitoribosome in the Spotlight
  Tomal, Cells 2019
  • “...uL23m AT4G39880 uL24m AT5G23535 bL25m 1 AT4G23620 AT5G66860 bL27m AT2G16930 bL28m AT4G31460 uL29m AT1G07830 uL30m AT5G55140 bL31m 1 AT5G55125 AT1G27435 bL33m AT5G18790 bL36m AT5G20180 mL40 AT4G05400 mL41 1 AT5G40080 AT5G39800 mL43 AT3G59650 mL46 AT1G14620 mL53 AT5G39600 mL54 AT3G01740 mL101 (rPPR4 3 ) AT1G60770 mL102 (rPPR5 3...”

6xywAz / Q8L908 6xywAz (see paper)
39% identity, 68% coverage

• Ligand: rna (6xywAz)

FTH_0249 ribosomal protein L30 from Francisella tularensis subsp. holarctica OSU18
FTN_0257 50S ribosomal protein L30 from Francisella tularensis subsp. novicida U112
41% identity, 89% coverage

• Use of magnetic hydrazide-modified polymer microspheres for enrichment of Francisella tularensis glycoproteins
  Horák, Soft matter 2012
  • “...cyt FTH_0247 Ribosomal protein L18 13.04/9.97 cyt cyt FTH_0248 Ribosomal protein S5 17.56/9.99 cyt cyt FTH_0249 50S ribosomal protein L30 6.87/10.09 cyt cyt FTH_0250 Ribosomal protein L15 15.10/10.24 cyt cyt FTH_0251 Preprotein translocase subunit secY 48.46/10.01 CM TMH FTH_0253 Ribosomal protein S13 13.38/11.54 cyt cyt FTH_0254...”
• Importance of host cell arginine uptake in Francisella phagosomal escape and ribosomal protein amounts
  Ramond, Molecular & cellular proteomics : MCP 2015
  • “...FTN_1335 FTN_1288 FTN_0916 FTN_0676 FTN_0675 FTN_0608 FTN_0265 FTN_0257 FTN_0256 FTN_0247 FTN_0243 FTN_0242 FTN_0235 FTN_0159 rpsP rpmE rpsK rpsM rplN rplP rpsC...”

PD0455 50S ribosomal protein L30 from Xylella fastidiosa Temecula1
42% identity, 90% coverage

• Characterization of regulatory pathways in Xylella fastidiosa: genes and phenotypes controlled by algU
  Shi, Applied and environmental microbiology 2007
  • “...rpmE PD2123 PD0439 PD0444 PD0445 PD0447 PD0450 PD0451 PD0452 PD0454 PD0455 PD0458 PD0488 PD0489 PD0749 50S 50S 50S 50S 50S 30S 30S 50S 30S 50S 30S 50S 50S 50S...”

ZMO0534 50S ribosomal protein L30 from Zymomonas mobilis subsp. mobilis ZM4
46% identity, 97% coverage

• Investigation of the impact of a broad range of temperatures on the physiological and transcriptional profiles of Zymomonas mobilis ZM4 for high-temperature-tolerant recombinant strain development
  Li, Biotechnology for biofuels 2021
  • “...ZMO0008 ), as well as ribosome protein-related genes ( ZMO0884 , ZMO0532 , ZMO1079 , ZMO0534 , and ZMO1145 ). The down-regulation of genes related to glucose metabolism at high temperature was consistent with the decrease of glucose consumption in ZM4 at high temperature (Fig. 2...”

BAB1_1237 Ribosomal protein L30:Ribosomal protein L30, bacterial and organelle form from Brucella melitensis biovar Abortus 2308
BMEI0775 LSU ribosomal protein L30P from Brucella melitensis 16M
47% identity, 75% coverage

• Proteomics-based confirmation of protein expression and correction of annotation errors in the Brucella abortus genome
  Lamontagne, BMC genomics 2010
  • “...able to almost fully reconstitute one of the two ribosomal RNA operons, with all but BAB1_1237 found. Additionally, the previously mentioned BAB1_1645 and BAB1_1646 genes are predicted to be part of an operon containing 6 genes, BAB1_1645 to BAB1_1650 http://www.microbesonline.org/operons/gnc359391.html . Four of these proteins were...”
• Intracellular adaptation of Brucella abortus
  Lamontagne, Journal of proteome research 2009
  • “...29 BAB1_1181 Protein synthesis Frr 29 BAB1_2063 Protein synthesis TrmE 29 BAB1_1205 Unknown ElaB-domain 30 BAB1_1237 Protein synthesis LSU L30 30 BAB2_0888 Nucleotide metab Nrd 30 BAB1_1457 Unknown Unknown 31 BAB1_1251 Protein synthesis SSU S19 31 BAB1_1063 Nucleotide metab NrdA 32 BAB1_0025 Protein synthesis SSU S1...”
• Ultrasensitive Detection of Pathogenic Bacteria by Targeting High Copy Signature Genes
  Dong, Frontiers in veterinary science 2022
  • “...each of the strains have 5 to 13 copies of IS711. Compared with the BMEI1001, BMEI0775 and BMEI0027, the assays of high copy genes IS711 showed higher sensitivity and is an ideal high copy signature gene for Brucella . Detection of clinical samples with assays targeting...”
  • “...numbers for further analysis. A high copy recombinase gene BMEI1001 (seven copies), low copy gene BMEI0775 (two copies), insertion sequence IS711 (six copies), and single copy gene BMEI0027 (one copy) were selected for comparison ( Figure 2A ). Primers for these genes were designed and synthesized...”

6yweU / Q8X098 structure of the mitoribosome from Neurospora crassa in the P/E tRNA bound state (see paper)
44% identity, 40% coverage

• Ligand: rna (6yweU)

PP0472, PP_0472 ribosomal protein L30 from Pseudomonas putida KT2440
39% identity, 97% coverage

• UEG Week 2024 Poster Presentations
  , United European gastroenterology journal 2024
• UEG Week 2023 Poster Presentations
  , United European gastroenterology journal 2023
• H-NS Family Proteins Drastically Change Their Targets in Response to the Horizontal Transfer of the Catabolic Plasmid pCAR1
  Nakamura, Frontiers in microbiology 2020
  • “...ribosomal protein S3 PP_0463 rpsQ 30S ribosomal protein S17 PP_0469 rplF 50S ribosomal protein L6 PP_0472 rpmD 50S ribosomal protein L30 PP_0473 rplO 50S ribosomal protein L15 PP_0475 rpmJ 50S ribosomal protein L36 PP_0476 rpsM 30S ribosomal protein S13 PP_0477 rpsK 30S ribosomal protein S11 PP_0478...”

AFUA_4G10480 50S ribosomal protein L30, putative from Aspergillus fumigatus Af293
41% identity, 62% coverage

• Identification of Antifungal Targets Based on Computer Modeling
  Bencurova, Journal of fungi (Basel, Switzerland) 2018
  • “...searches. This approach identified cytochrome c oxidase family protein (AFUA_3G14440) and 50S ribosomal protein L30 (AFUA_4G10480) as essential genes whose products can be a potential antimycotic targets [ 28 ]. 3.4. Ranking and Prioritization Criteria The selected list of best potential drug targets can be scored...”
  • “...antimycotic potential [ 104 ]. The pipeline identified two essential genes, the 50S ribosomal protein (AFUA_4G10480), and a cytochrome c oxidase family protein (AFUA_3G14440) that participate in oxidative phosphorylation, as good targets. Some of the targets are currently under experimental evaluation, such as 2,3-bisphosphoglycerate-independent phosphoglycerate mutase...”
• Systematic Identification of Anti-Fungal Drug Targets by a Metabolic Network Approach
  Kaltdorf, Frontiers in molecular biosciences 2016
  • “...SUC Alpha,alpha-trehalose-phosphate synthase subunit ESSENTIAL GENES AFUA_3G14440 0.916 1.174 n.s. Cytochrome c oxidase family protein AFUA_4G10480 n.s. 2.375 1.812 Mitochondrial large ribosomal subunit protein L30 logFC: -1 1 a Only genes are listed that resulted from two ranking functions (RhumPDB + Expression, Supplementary Table 14 ;...”
  • “...important metabolic genes. Two preliminary targets identified in this way include the 50S ribosomal protein (AFUA_4G10480) and a cytochrome c oxidase family protein (AFUA_3G14440) that participates in oxidative phosphorylation. Target ranking and identification A total of 130 metabolism-associated A. fumigatus proteins were identified and subsequently parsed...”

8cd1Z / Q9HWF3 8cd1Z (see paper)
39% identity, 95% coverage

• Ligand: rna (8cd1Z)

New Search

Statistics

How It Works

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

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

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

PaperBLAST also incorporates manually-curated protein functions:

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

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

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

Changes to PaperBLAST since the paper was written:

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

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

Secrets

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

Omissions from the PaperBLAST Database

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

References

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

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

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

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

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

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

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

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

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

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

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

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