PaperBLAST

PaperBLAST Hits for A4VVU6 Large ribosomal subunit protein bL35 (Streptococcus suis (strain 05ZYH33)) (66 a.a., MPKQKTHRAS...)

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>A4VVU6 Large ribosomal subunit protein bL35 (Streptococcus suis (strain 05ZYH33))
MPKQKTHRASAKRFKRTGSGGLKRFRAYTSHRFHGKTKKQRRHLRKAGMVHAGDFKRIKS
MLTGLK

Running BLASTp...

Found 43 similar proteins in the literature:

A4VVU6 Large ribosomal subunit protein bL35 from Streptococcus suis (strain 05ZYH33)
SSU05_1269 50S ribosomal protein L35 from Streptococcus suis 05ZYH33
100% identity, 100% coverage

• DivIVA Interacts with the Cell Wall Hydrolase MltG To Regulate Peptidoglycan Synthesis in Streptococcus suis
  Jiang, Microbiology spectrum 2023
  • “...Uncharacterized protein conserved in bacteria 14.605 1.9804 ++ A4VXU5 SSU05_1968 DNA nuclease 113.94 1.9637 ++ A4VVU6 SSU05_1269 rpmI 50S ribosomal protein L35 7.6911 1.9 ++ A4VW87 SSU05_1410 ftsX Cell division protein FtsX 35.393 1.8979 ++ A4VSW9 SSU05_0240 msrA Multifunctional fusion protein 35.624 1.7385 + A4VSW2 SSU05_0233...”
• DivIVA Interacts with the Cell Wall Hydrolase MltG To Regulate Peptidoglycan Synthesis in Streptococcus suis
  Jiang, Microbiology spectrum 2023
  • “...protein conserved in bacteria 14.605 1.9804 ++ A4VXU5 SSU05_1968 DNA nuclease 113.94 1.9637 ++ A4VVU6 SSU05_1269 rpmI 50S ribosomal protein L35 7.6911 1.9 ++ A4VW87 SSU05_1410 ftsX Cell division protein FtsX 35.393 1.8979 ++ A4VSW9 SSU05_0240 msrA Multifunctional fusion protein 35.624 1.7385 + A4VSW2 SSU05_0233 Uncharacterized...”

spr0862 50S Ribosomal protein L35 from Streptococcus pneumoniae R6
92% identity, 100% coverage

• 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
  • “...spr0194 spr0196 spr0197 spr0200 spr0201 spr0204 spr0205 spr0555 spr0682 spr0862 spr0863 spr1212 spr1394 1.9 1.4 1.5 1.6 1.6 1.6 1.7 1.8 1.7 1.7 1.9 1.7 1.7 1.6...”

SPy0805 50S ribosomal protein L35 from Streptococcus pyogenes M1 GAS
91% identity, 98% coverage

• Characterization of the RofA regulon in the pandemic M1_global and emergent M1_UK lineages of Streptococcus pyogenes
  Zhi, Microbial genomics 2023
  • “...protein 1.392 0.003 1.176 0.002 Spy0635 rpmA LSU ribosomal protein L27P 0.710 0.020 0.659 0.037 Spy0805 srtK Nisin biosynthesis sensor protein 0.655 0.011 0.680 0.017 Spy0985 na phnA protein 0.947 0.006 0.894 0.012 Spy1087 na Putative cytosolic protein 1.889 0.005 2.208 <0.001 Spy1089 na Hypothetical protein...”

Q3K0C9 Large ribosomal subunit protein bL35 from Streptococcus agalactiae serotype Ia (strain ATCC 27591 / A909 / CDC SS700)
91% identity, 100% coverage

• Downregulation of Ribosomal Contents and Kinase Activities Is Associated with the Inhibitive Effect on the Growth of Group B Streptococcus Induced by Placental Extracellular Vesicles
  Gao, Biology 2021
  • “...30S ribosomal protein S1, nucleic acid binding A0A6A4TZH8 down 50S ribosomal protein L3, rRNA binding Q3K0C9 down 50S ribosomal protein L35, structural constituent of ribosome Q8DYG1 down 50S ribosomal protein L11, large ribosomal subunit rRNA binding Q8DZZ2 down 30S ribosomal protein S20, rRNA binding R4Z934 down...”

D0R5D2 Large ribosomal subunit protein bL35 from Lactobacillus johnsonii (strain FI9785)
79% identity, 100% coverage

• Identification of Genes Required for Glucan Exopolysaccharide Production in Lactobacillus johnsonii Suggests a Novel Biosynthesis Mechanism
  Mayer, Applied and environmental microbiology 2020
  • “...aminoacylation D0R3G2 30S ribosomal protein S16 rpsP 5 11 227 0.73 1.66 0.60 X Translation D0R5D2 50S ribosomal protein L35 rpmL 7 8 80 0.69 1.61 0.62 X Translation D0R4W9 ATP synthase subunit b atpF 7 18 42 0.65 1.57 0.64 X ATP biosynthetic process; ion...”

5myjB7 / A2RMR2 of 70S ribosome from Lactococcus lactis (see paper)
80% identity, 97% coverage

• Ligand: rna (5myjB7)

IUJ47_RS07500 50S ribosomal protein L35 from Enterococcus faecalis
74% identity, 100% coverage

• Antibacterial Components and Modes of the Methanol-Phase Extract from Commelina communis Linn
  Liu, Plants (Basel, Switzerland) 2023
  • “...ribosomal protein L29 IUJ47_RS04640 0.195 50S ribosomal protein L36 IUJ47_RS04530 0.201 50S ribosomal protein L4 IUJ47_RS07500 0.222 50S ribosomal protein L35 IUJ47_RS01420 0.226 50S ribosomal protein L33 IUJ47_RS04645 0.229 30S ribosomal protein S13 IUJ47_RS04540 0.233 50S ribosomal protein L2 IUJ47_RS04560 0.233 50S ribosomal protein L16 IUJ47_RS04520...”

7nhk7 / A0A1B4XM73 7nhk7 (see paper)
76% identity, 94% coverage

• Ligand: rna (7nhk7)

RL35_BACSU / P55874 Large ribosomal subunit protein bL35; 50S ribosomal protein L35 from Bacillus subtilis (strain 168) (see paper)
BSU28860 50S ribosomal protein L35 from Bacillus subtilis subsp. subtilis str. 168
68% identity, 100% coverage

• subunit: Part of the 50S ribosomal subunit.
• Arginine phosphorylation marks proteins for degradation by a Clp protease
  Trentini, Nature 2016
  • “...O31461 ilvE Branched-chain aa transaminase 1 T249 P42956 mtlA PTS system mannitol-specific EIICB S365 S365 P55874 rpmI 50S ribosomal prot. L35 S47 S47 P21476 rpsS 30S ribosomal prot. S19 T77 O34607 sdaAA Probable L-serine dehydratase, chain T99 P54334 xkdO Phage-like element PBSX prot. XkdO S295 O34833...”
• Proteomics analyses of Bacillus subtilis after treatment with plumbagin, a plant-derived naphthoquinone
  Reddy, Omics : a journal of integrative biology 2015
  • “...OS O34967 50S ribosomal protein L31 type B OS P55874 50S ribosomal protein L35 OS a Gene name Q-TOF Unique Plumbagin/ Unique Plumbagin/ Coverage peptides...”
• The Blueprint of a Minimal Cell: MiniBacillus
  Reuß, Microbiology and molecular biology reviews : MMBR 2016
  • “...BSU01340 BSU37070 BSU15080 BSU24900 BSU00990 BSU41060 BSU28860 BSU01400 BSU16490 BSU01220 BSU29660 BSU01330 BSU40910 BSU01110 BSU01300 BSU01500 BSU01150...”

GBAA_4818 50S ribosomal protein L35 from Bacillus anthracis str. 'Ames Ancestor'
70% identity, 100% coverage

• Microevolution of Anthrax from a Young Ancestor (M.A.Y.A.) Suggests a Soil-Borne Life Cycle of Bacillus anthracis
  Braun, PloS one 2015
  • “...Phe comG operon protein 4 GBAA_4463 6 4380690 A C - 1 ribosomal protein L35 GBAA_4818 1 silent mutation HRM for analysis of SNP distribution in Pollino isolates SNP discovery in the genome-sequenced Pollino isolates yielded a number of 6 point mutations that appeared to be...”

8buu3 / P55874 8buu3 (see paper)
68% identity, 98% coverage

• Ligand: rna (8buu3)

Q71YN4 Large ribosomal subunit protein bL35 from Listeria monocytogenes serotype 4b (strain F2365)
lmo1784 ribosomal protein L35 from Listeria monocytogenes EGD-e
65% identity, 100% coverage

• Proteomic Exploration of Listeria monocytogenes for the Purpose of Vaccine Designing Using a Reverse Vaccinology Approach
  Srivastava, International journal of peptide research and therapeutics 2021
  • “...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 143 Q71ZJ5 0.952 Non-allergen...”
  • “...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 50.8 2.0807 Antigen DRB1_1301 KKYCPRLRR 61.5...”
• Comparison of Surface Proteomes of Adherence Variants of Listeria Monocytogenes Using LC-MS/MS for Identification of Potential Surface Adhesins
  Tiong, Pathogens (Basel, Switzerland) 2016
  • “...protein S20 (9) CY CY 0.33 (E,C,CM) CY No No 0 No No <1.8 0.83 lmo1784 (3.7.1) 50S ribosomal protein L35 (8) CY CY 0.33 (E,C,CM) CY No No 0 Yes No <1.8 1.22 lmo2156 (5.1) Hypothetical protein (13) S M (Equal score to all) Unknown...”
  • “...--- 10 19 lmo1699 * ,1 lmo1699 Mobility and chemotaxis 1.5 --- >10 --- 20 lmo1784 rpmI Ribosomal proteins 3.7.1 --- --- 21 lmo1860 msrA Protein modification reductase A 3.8 --- 10x --- 22 lmo1953 pnp Metabolism of nucleotides and nucleic acids 2.3 --- >10 ---...”
• Characterisation of the transcriptomes of genetically diverse Listeria monocytogenes exposed to hyperosmotic and low temperature conditions reveal global stress-adaptation mechanisms
  Durack, PloS one 2013
  • “...lmo1707 1.95 *** 1.56 ** 1.10 *** 1.81 *** 1.08 *** 1.26 *** unknown protein lmo1784 rpmI 2.39 *** 1.32 *** 1.80 *** 1.66 ** 1.38 *** 2.32 *** ribosomal protein L35 lmo1816 rpmB 3.27 *** 4.34 *** 3.01 *** 3.58 ** 1.84 *** 4.11 ***...”
  • “...were rplK ( lmo0248 ), rplA ( lmo0249 ), rpsD ( lmo1596 ), rpmI ( lmo1784 ), rpmB ( lmo1816 ) and rpmE ( lmo2548 ). Although different physical stresses, both high Na + concentration and low temperature have a damaging effect on ribosome function. While...”
• Transcriptomic and phenotypic analyses suggest a network between the transcriptional regulators HrcA and sigmaB in Listeria monocytogenes
  Hu, Applied and environmental microbiology 2007
  • “...lmo1523 lmo1542 lmo1541 lmo1657 lmo1658 lmo1683 lmo1785 lmo1784 lmo1859 lmo1879 lmo1921 lmo1956 lmo2048 lmo2047 lmo2055 lmo2054 lmo2261 lmo2340 lmo2362 lmo2363...”

8uu97 / A0A660JIB9 8uu97 (see paper)
65% identity, 98% coverage

• Ligand: rna (8uu97)

SACOL1726 ribosomal protein L35 from Staphylococcus aureus subsp. aureus COL
P66276 Large ribosomal subunit protein bL35 from Staphylococcus aureus (strain N315)
Q6GG26 Large ribosomal subunit protein bL35 from Staphylococcus aureus (strain MRSA252)
SA1503 50S ribosomal protein L35 from Staphylococcus aureus subsp. aureus N315
SAV1679 50S ribosomal protein L35 from Staphylococcus aureus subsp. aureus Mu50
MW1623 50S ribosomal protein L35 from Staphylococcus aureus subsp. aureus MW2
EKM74_RS01860 50S ribosomal protein L35 from Staphylococcus aureus
61% identity, 94% coverage

• Tea tree oil-induced transcriptional alterations in Staphylococcus aureus
  Cuaron, Phytotherapy research : PTR 2013
  • “...adenylosuccinate synthase SACOL0018 5-GAGGTTGGTCGTGAATACGG-3 5-TGGGTACTCAGTAATTTCTTTACCG-3 purM phosphoribosylaminoimidazole synthetase SACOL1080 5-AATATGGGTATTGGCTATACGG-3 5-CACAATATGACCAATTTGATAGGC-3 rpmI ribosomal protein L35 SACOL1726 5-TGCCAAAAATGAAAACTCACC-3 5-GAGATGTGAAAGCTCTTGAACG-3 tenA transcriptional regulator, TenA family SACOL2086 5-TAGGAGCTGACGCATTACGC-3 5-CCCATTGTTCTAGTGTCATAGCC-3 vraR DNA-binding response regulator VraR SACOL1942 5-AAAGAAGCAATTGCCAAAGC-3 5-TGAGTCGTCGCTTCTACACC-3 vraS histidine kinase sensor SACOL1943 5-AGTGCCGATGAAAGTTGTGC-3 5-TTTTGTACCGTTTGAATGACG-3 vraX VraX protein SACOL0625 5-TCGACAGTATCACCATGAAGG-3...”
  • “...dehydrogenase SACOL2628 7.0 1.5 1.6 hypothetical protein (191 aa) SACOL1086 7.0 rpmI ribosomal protein L35 SACOL1726 5.9 2.0 1.8 thiD phosphomethylpyrimidine kinase SACOL2085 5.1 purQ phosphoribosylformylglycinamidine synthase I SACOL1077 4.9 purC phosphoribosylaminoimidazole-succinocarboxamide synthase SACOL1075 4.6 thiE putative thiamine-phosphate pyrophosphorylase SACOL2083 3.8 thiM hydroxyethylthiazole kinase SACOL2084 3.2...”
• The Staphylococcus aureus LytSR two-component regulatory system affects biofilm formation
  Sharma-Kuinkel, Journal of bacteriology 2009
  • “...SACOL2234 SACOL2237 SACOL2228 SACOL2231 SACOL2221 SACOL1726 SACOL1274 SACOL2233 SACOL2222 SACOL0592 SACOL2240 SACOL2214 SACOL0591 SACOL2226 SACOL1292 SACOL2230...”
• Identification of N-terminal protein processing sites by chemical labeling mass spectrometry
  Misal, Rapid communications in mass spectrometry : RCM 2019
  • “...24 M AIKKYKPITNGR R P60432 Ribosomal protein L2 Cytoplasm 21 19 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...”
• Structural and Functional Dynamics of Staphylococcus aureus Biofilms and Biofilm Matrix Proteins on Different Clinical Materials
  Hiltunen, Microorganisms 2019
  • “...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 50S ribosomal protein L9 Q6GKT0 Elongation factor TuEfTU Q6GJC0 Elongation...”
• Transcriptional profiles of the response of methicillin-resistant Staphylococcus aureus to pentacyclic triterpenoids
  Chung, PloS one 2013
  • “...50S ribosomal protein L33 1,2,3 8.4 Translation SAS093 rpmH 50S ribosomal protein L34 6.3 Translation SA1503 rpmI 50S ribosomal protein L35 6.0 Translation SAS078 rpmJ 50S ribosomal protein L36 21.0 Translation SA2035 rplE 50S ribosomal protein L5 6.3 Translation SA0498 rplL 50S ribosomal protein L7/L12 8.3...”
• Staphylococcus aureus virulence expression is impaired by Lactococcus lactis in mixed cultures
  Even, Applied and environmental microbiology 2009
  • “...and cellular division genes SAV0535 SAV0547 SAV0548 SAV1678 SAV1679 SAV1128 IGS2 SAV1180 SAV0511 Corresponding ORF (MW2)c 4464 EVEN ET AL. APPL. ENVIRON....”
• Staphylococcus aureus virulence expression is impaired by Lactococcus lactis in mixed cultures
  Even, Applied and environmental microbiology 2009
  • “...SAV1433 SAV1474 SAV1261 SAV1228 MW0491 MW0502 MW0503 MW1622 MW1623 MW1010 nusG fus tufA rplT rpmI rpmF MW1063 MW0466 ftsL ftsH MW0284 MW1323 MW1363 MW1144...”
• Transcriptomic Analysis Revealed Antimicrobial Mechanisms of Lactobacillus rhamnosus SCB0119 against Escherichia coli and Staphylococcus aureus
  Peng, International journal of molecular sciences 2022
  • “...ribosomal protein L21 EKM74_RS01855 19.42 10.05 621.08 94.23 4.999194 rplT ; 50S ribosomal protein L20 EKM74_RS01860 51.94 21.24 5478.49 45.03 6.720704 rpmI ; 50S ribosomal protein L35 EKM74_RS02080 80.66 17.27 3451.94 642.32 5.419314 rpsD ; 30S ribosomal protein S4 EKM74_RS05465 190.13 11.18 3317.01 500.37 4.124828 rpsI...”

5nrg3 / Q2FXQ0 The crystal structure of the large ribosomal subunit of staphylococcus aureus in complex with rb02 (see paper)
61% identity, 92% coverage

• Ligands: rna; manganese (ii) ion (5nrg3)

lp_1516 ribosomal protein L35 from Lactobacillus plantarum WCFS1
65% identity, 77% coverage

• Response of Lactobacillus plantarum WCFS1 to the Gram-Negative Pathogen-Associated Quorum Sensing Molecule N-3-Oxododecanoyl Homoserine Lactone
  Spangler, Frontiers in microbiology 2019
  • “...0.19 RL28_LACPL lp_1624 rpmB 50S ribosomal protein L28 -0.18 0.016 -0.24 0.27 0.27 0.15 RL35_LACPL lp_1516 rpmI 50S ribosomal protein L35 0.046 0.44 -0.33 0.22 0.08 0.15 RL6_LACPL lp_1051 rplF 50S ribosomal protein L6 0.079 0.935 -0.58 2.37 0.62 0.31 RS11_LACPL lp_1061 rpsK 30S ribosomal protein...”

7ood1 / P75447 Mycoplasma pneumoniae 50s subunit of ribosomes in chloramphenicol- treated cells (see paper)
MPN116 ribosomal protein L35 from Mycoplasma pneumoniae M129
57% identity, 88% coverage

• Ligand: rna (7ood1)
• Quantitative essentiality in a reduced genome: a functional, regulatory and structural fitness map
  Miravet-Verde, 2025
• FASTQINS and ANUBIS: two bioinformatic tools to explore facts and artifacts in transposon sequencing and essentiality studies
  Miravet-Verde, Nucleic acids research 2020
  • “...terminal regions for E and F genes becomes shorter with each cell passage. For example, mpn116 is predicted to be a F gene ( Poisson model, default) up to P06, at which point it starts to be classified as E using the arbitrary threshold of 5%...”
  • “...the CPD algorithm. Base-pair scales are shown below the gene name. ( A ) Gene mpn116 at different passages, for passages 02, 06 and 08 (darker to lighter colors), presents and extended C-terminal of 50% (passage 1 and 2) that becomes shorter with selection (15% for...”
• Development of a Multilocus Sequence Typing Scheme for Molecular Typing of Mycoplasma pneumoniae
  Brown, Journal of clinical microbiology 2015
  • “...MPN016b MPN017b MPN020 MPN103 MPN105 MPN108 MPN109 MPN113 MPN116 MPN118 MPN120 MPN122 MPN136 MPN004 MPN104c MPN106c MPN110c MPN124 MPN131 MPN111 MPN011 MPN112...”
  • “...MPN113 MPN111 MPN108 MPN118 MPN103 MPN120 MPN136 MPN130 MPN116 MPN105 MPN109 MPN122 MPN101 MPN106 MPN124 MPN110 MPN131 MPN104 MPN126 MPN128 MPN102 MPN129 MPN134...”

SYNW0058 50S ribosomal protein L35 from Synechococcus sp. WH 8102
50% identity, 94% coverage

• Coastal strains of marine Synechococcus species exhibit increased tolerance to copper shock and a distinctive transcriptional response relative to those of open-ocean strains
  Stuart, Applied and environmental microbiology 2009
  • “...1.11 SYNW1960 SYNW0144 SYNW0334 SYNW2232 SYNW1303 SYNW2224 SYNW0058 SYNW0546 SYNW0521 SYNW2442 SYNW2375 SYNW0233 SYNW2103 SYNW1730 SYNW1778 SYNW2489 0.46 0.59...”

sync_0059 ribosomal protein L35 from Synechococcus sp. CC9311
47% identity, 94% coverage

• Selection in coastal Synechococcus (cyanobacteria) populations evaluated from environmental metagenomes
  Tai, PloS one 2011
  • “...2.046 3.161 100/14.9 A N Y sync_2711 lipoprotein, putative 0.275 2.556 75/5.4 A N N sync_0059 ribosomal protein L35 Inf Inf 72/8.1 C N N sync_0536 PsbM Inf Inf 43/4.4 C N Y sync_0637 conserved hypothetical Inf Inf 0.5/0.5 A N Y sync_0780 hypothetical Inf Inf...”
  • “...and 2 ). For example, only non-synonymous polymorphisms were observed for the ribosomal protein L35 (sync_0059) ( Table 1 ): histidine (hydrophilic, positively charged) to glutamine (hydrophilic, neutral) and proline (hydrophobic neutral) to alanine (hydrophobic neutral). A putative lipoprotein (sync_2711) has a dN/dS<1, but relative to...”
• Coastal strains of marine Synechococcus species exhibit increased tolerance to copper shock and a distinctive transcriptional response relative to those of open-ocean strains
  Stuart, Applied and environmental microbiology 2009
  • “...sync_0133 sync_2496 sync_2586 sync_1422 sync_1542 sync_0059 sync_2224 sync_2274 sync_2872 sync_2789 sync_0271 sync_0950 sync_1807 sync_2027 sync_2900 0.54...”

ISORED2_02500 50S ribosomal protein L35 from Acetobacterium wieringae
47% identity, 99% coverage

• Evidence for a Putative Isoprene Reductase in Acetobacterium wieringae
  Kronen, mSystems 2023
  • “...Stress response ISORED2_01001 VUZ28314.1 2.39 1.01 10 2 556 ENOG4105CKU Formyltetrahydrofolate synthetase One-carbon metabolic process ISORED2_02500 VUZ24737.1 2.44 2.62 10 2 67 ENOG4105VJV 50s ribosomal protein L35 Structural constituent of ribosome ISORED2_00772 VUZ28022.1 2.46 2.85 10 2 513 ENOG410ND7V Xylulokinase Carbohydrate metabolic process ISORED2_00996 VUZ28309.1 4.48...”

lpp2768 50S ribosomal protein L35 from Legionella pneumophila str. Paris
48% identity, 97% coverage

• Two small ncRNAs jointly govern virulence and transmission in Legionella pneumophila
  Sahr, Molecular microbiology 2009
  • “...- lpp2828 NADH-quinone oxidoreductase chain I 1.99 - lpp2827 NADH-quinone oxidoreductase chain J 2.42 - lpp2768 50S ribosomal protein L35 3.06 2.88 lpp2689 30S ribosomal subunit protein S2 3.33 1.78 lpp2026 Peptidoglycan-associated lipoprotein precursor 1.79 4.52 lpp1958 Major outer membrane protein 2.16 6.57 lpp1773 Similar to...”

azo1081 50S ribosomal protein L35 from Azoarcus sp. BH72
48% identity, 94% coverage

• Environmental factors affecting the expression of pilAB as well as the proteome and transcriptome of the grass endophyte Azoarcus sp. strain BH72
  Hauberg-Lotte, PloS one 2012
  • “...quadruplicates; five positive controls were spotted in additional replicates ( azo1072 (30S ribosomal protein S1), azo1081 (50S ribosomal protein L35), azo2104 (30S ribosomal protein S15), azo2837 (probable glyceraldehyde 3-phosphate dehydrogenase) and azo2898 (30S ribosomal protein S16). Negative buffer controls, as well as negative controls consisting of...”

MHO_1280 50S ribosomal protein L35 from Mycoplasma hominis
47% identity, 94% coverage

• Characterisation of mobile genetic elements in Mycoplasma hominis with the description of ICEHo-II, a variant mycoplasma integrative and conjugative element
  Henrich, Mobile DNA 2020
  • “...(IA)) and ICEF-II-A (AAN85259.1 (II-A)). Two chromosomal proteins of M. hominis PG21 (MHO_0070 (CAX37141.1) and MHO_1280 (CAX37262.1)) were used as unrelated ICE-outliners in ClustalW-based Multiple Sequence Alignment. A. Phylogenetic tree; B. Percent amino acid identities and divergences; and C. Multiple Sequence Alignment of CDS6 encoded proteins....”
• Genome-wide Analysis of Mycoplasma hominis for the Identification of Putative Therapeutic Targets
  Parvege, Drug target insights 2014
  • “...Novel 27 MHO_1120 30S ribosomal protein S6 Cytoplasm 0 No (59) 32 No Novel 28 MHO_1280 50S ribosomal protein L35 Cytoplasm 0 No (72) 31 No Novel 29 MHO_1180 Phenylalanyl-trna synthetase subunit beta Cytoplasm 0 Yes (116) 32 No Druggable 30 MHO_0050 DNA polymerase III subunit...”

SG1420 50S ribosomal protein L35 from Sodalis glossinidius str. 'morsitans'
53% identity, 83% coverage

• Quorum sensing primes the oxidative stress response in the insect endosymbiont, Sodalis glossinidius
  Pontes, PloS one 2008
  • “...genes encoding subunits of the 30S (SG0380, SG0412 and SG2269) and 50S ribosomal proteins (SG0133, SG1420, SG1421, SG1572, SG2207, SG2252, SG2270, SG2271 and SG2273). In addition, genes encoding a 16S rRNA pseudouridylate synthase A (SG1570), a tRNA/rRNA methyltransferase (SG1908) and a putative ribosome modulation factor (SG1025)...”

HSM_1355 50S ribosomal protein L35 from Haemophilus somnus 2336
HSM_1355 50S ribosomal protein L35 from Histophilus somni 2336
52% identity, 82% coverage

• RNA-seq based transcriptional map of bovine respiratory disease pathogen "Histophilus somni 2336"
  Kumar, PloS one 2012
  • “.... 10.1371/journal.pone.0029435.g005 Figure 5 Identification of a novel operon structure comprised of three genes: HSM_1354, HSM_1355, and HSM_1356. The RNA-Seq coverage shows three genes annotated as ribosomal proteins (IF3, L35, and L20) being expressed as a transcription unit. Discussion In this study using RNA-Seq we describe...”

PMCN03_0605 50S ribosomal protein L35 from Pasteurella multocida subsp. multocida str. HB03
HI1319m ribosomal protein L35 from Haemophilus influenzae Rd KW20
52% identity, 82% coverage

• Genomic and transcriptomics analysis reveal putative secreted proteins expressed of <i>Pasteurella multocida</i> during 18β-glycyrrhetinic acid treatment
  Wu, Frontiers in veterinary science 2024
  • “...6 PMCN03_0519 30S ribosomal protein S9, rps9 7 PMCN03_0521 Stringent starvation protein B, sspB 8 PMCN03_0605 50S ribosomal protein L35, rpl35 9 PMCN03_0606 50S ribosomal protein L20, rpl20 10 PMCN03_0622 Phohoribosylaminoimidazole carboxylase catalytic subunit, purE 11 PMCN03_0914 Dihydrolipoamide acetyltransferase, aceF 12 PMCN03_1019 50S ribosomal protein L31...”
• Initial proteome analysis of model microorganism Haemophilus influenzae strain Rd KW20
  Kolker, Journal of bacteriology 2003
  • “...HI0779 HI0789 HI1630 HI0879 HI0951 HI0785 HI0796 HI0758 HI0158 HI0950 HI0998 HI1319m HI0798.1 550 252 236 207 167 131 157 131 131 119 130 125 123 102 90 83 86...”

BTH_I2593 ribosomal protein L35 from Burkholderia thailandensis E264
BPSL1943 50S ribosomal protein L35 from Burkholderia pseudomallei K96243
bglu_1g21500 Ribosomal protein L35 from Burkholderia glumae BGR1
44% identity, 94% coverage

• Gene and protein expression in response to different growth temperatures and oxygen availability in Burkholderia thailandensis
  Peano, PloS one 2014
  • “...4.92 2.3 150 All BTH_I2592 ( rplT ) L20 4.59 2.2 All rplT rpmI [33] BTH_I2593 ( rpmI ) L35 3.48 1.8 All rplT rpmI [33] BTH_I3041 ( rplQ ) L17 3.25 1.7 All BTH_I3043 ( rpsD ) S4 3.73 1.9 129.1 All [33] BTH_I3049BTH_I3058 (...”
• Unraveling the role of toxin-antitoxin systems in <i>Burkholderia pseudomallei</i>: exploring bacterial pathogenesis and interactions within the HigBA families
  Chapartegui-González, Microbiology spectrum 2024
  • “...and BPSS0390 (toxin HicA), and different genes that encodes for ribosomal-related proteins (BPSL0915, BPSL1461, BPSL1942, BPSL1943, BPSL2444, BPSL3194, BPSL3196, BPSL3197, BPSL3209, and BPSL3217). It is important to highlight a putative new TA system, encoded by BPSS1821-BPSS1820, that exhibits identity homology with the MbcTA system from M....”
• Genetic and transcriptional analysis of the siderophore malleobactin biosynthesis and transport genes in the human pathogen Burkholderia pseudomallei K96243
  Alice, Journal of bacteriology 2006
  • “...involved in protein biosynthesis (e.g., BPSS1716, BPSL0915, BPSL1943, and BPSL1962) were down-regulated. ORFs BPSS1162 and BPSS1163 showed the widest change in...”
• RNAseq-based Transcriptome Analysis of Burkholderia glumae Quorum Sensing
  Kim, The plant pathology journal 2013
  • “...0.6 2 1.4 bglu_1g18160 rpsU 1 1.5 0.2 0.5 bglu_1g21490 rplT 1 0.8 1.4 1.1 bglu_1g21500 rpmI 1.3 0.9 1.3 1.2 bglu_1g25990 rpsO 0.6 0.5 1.5 1.6 bglu_1g28680 rpmB 0.7 0.6 1. 1 bglu_1g28690 rpmG 0.5 0.4 1.5 1.1 bglu_1g29160 rpsT 0.9 0.8 1.8 1.4 bglu_1g31330...”

F452_RS0103380 50S ribosomal protein L35 from Porphyromonas gulae DSM 15663
PGN_0964 probable 50S ribosomal protein L35 from Porphyromonas gingivalis ATCC 33277
PG0990 ribosomal protein L35 from Porphyromonas gingivalis W83
44% identity, 95% coverage

• Antibacterial effects of sodium tripolyphosphate against Porphyromonas species associated with periodontitis of companion animals
  Lee, Journal of veterinary science 2019
  • “...50S ribosomal protein L20 1.97E-26 +3.66 * F452_RS0100210 50S ribosomal protein L21 4.76E-35 +3.65 * F452_RS0103380 50S ribosomal protein L35 9.81E-24 +3.60 * F452_RS0102545 50S ribosomal protein L33 3.07E-20 +3.48 * F452_RS0102540 50S ribosomal protein L28 1.35E-14 +2.74 * F452_RS0101135 30S ribosomal protein S1 7.48E-15 +2.56...”
• Pathway analysis for intracellular Porphyromonas gingivalis using a strain ATCC 33277 specific database
  Hendrickson, BMC microbiology 2009
  • “...(1) PGN_0035 PGN_0167 PGN_0640 PGN_0965 PGN_0394 PGN_0188 PGN_0279 PGN_1572 PGN_1589 PGN_0636 PGN_0639 PGN_1647 PGN_1648 PGN_0641 PGN_0964 PGN_1698 PGN_1844 PGN_1088 PGN_1219 PGN_1651 PGN_1852 PGN_1573 PGN_1575 PGN_1853 PGN_1854 PGN_1588 PGN_1590 PGN_1855 PGN_1861 PGN_1832 PGN_1840 PGN_1863 PGN_1868 PGN_1842 PGN_1843 PGN_1872 PGN_1890 PGN_1849 PGN_1850 PGN_1891 PGN_1856 PGN_1857 PGN_1857 PGN_1858 PGN_1860...”
• Molecular pathways underlying inhibitory effect of antimicrobial peptide Nal-P-113 on bacteria biofilms formation of Porphyromonas gingivalis W83 by DNA microarray
  Wang, BMC microbiology 2017
  • “...synthetase is one of the key enzymes in protein synthesis [ 17 ]. PG2117 and PG0990 both encoding ribosomal proteins were shown to be up-regulated by 3.32-fold and 2.52-fold, respectively. Moreover, transporting and binding protein pathway was also significantly inhibited by Nal-P-113 treatment. 4 out of...”
• Microarray analysis of the transcriptional responses of Porphyromonas gingivalis to polyphosphate
  Moon, BMC microbiology 2014
  • “...protein L31 4.01 PG0656 50S ribosomal protein L34 6.80 PG0989 50S ribosomal protein L20 3.43 PG0990 Ribosomal protein L35 1.74 PG1723 Ribosomal protein S20 2.94 PG1758 Ribosomal protein S15 6.23 PG1959 Ribosomal protein L33 2.02 PG1960 Ribosomal protein L28 2.03 PG2117 30S ribosomal protein S16 2.93...”

RpmI / b1717 50S ribosomal subunit protein L35 from Escherichia coli K-12 substr. MG1655 (see 4 papers)
rpmI / P0A7Q1 50S ribosomal subunit protein L35 from Escherichia coli (strain K12) (see 14 papers)
RL35_ECOLI / P0A7Q1 Large ribosomal subunit protein bL35; 50S ribosomal protein L35; Ribosomal protein A from Escherichia coli (strain K12) (see 9 papers)
rpmI 50S ribosomal protein L35 from Escherichia coli K12 (see paper)
B1XG24 Large ribosomal subunit protein bL35 from Escherichia coli (strain K12 / DH10B)
B5XQC8 Large ribosomal subunit protein bL35 from Klebsiella pneumoniae (strain 342)
NP_416232 50S ribosomal subunit protein L35 from Escherichia coli str. K-12 substr. MG1655
STM1335 50S ribosomal subunit protein L35 from Salmonella typhimurium LT2
b1717 50S ribosomal subunit protein A from Escherichia coli str. K-12 substr. MG1655
NP_707397 50S ribosomal protein L35 from Shigella flexneri 2a str. 301
SEN1709 50S ribosomal subunit protein L35 from Salmonella enterica subsp. enterica serovar Enteritidis str. P125109
47% identity, 94% coverage

• subunit: Part of the 50S ribosomal subunit.
• Stress response of Escherichia coli to essential oil components - insights on low-molecular-weight proteins from MALDI-TOF
  Božik, Scientific reports 2018
  • “...to the chlorine- and peroxide-treated samples was that of 50S ribosomal protein L35 (m/z 7290,90, B1XG24), which is a structural constituent of the ribosome. This protein was also observed in cinnamaldehyde- and carene-treated samples. The lower amounts of stationary phase-induced ribosome-associated protein (m/z 5096,84, P68191, SRA)...”
• Combinatorial Antimicrobial Efficacy and Mechanism of Linalool Against Clinically Relevant Klebsiella pneumoniae
  Yang, Frontiers in microbiology 2021
  • “...2.61 A6TEW9 50S ribosomal protein L2 2.42 A6TEU2 Ribosomal RNA small subunit methyltransferase B 2.23 B5XQC8 50S ribosomal protein L35 2.09 A6T766 Ribosomal RNA large subunit methyltransferase I 2.00 A6THB4 50S ribosomal protein L9 1.97 A6THB1 30S ribosomal protein S6 1.65 Linalool Induces Oxidative Stress Which...”
• Antimicrobial activity and mode of action of terpene linalyl anthranilate against carbapenemase-producing Klebsiella pneumoniae
  Yang, Journal of pharmaceutical analysis 2021
  • “...L9 2.24 B5XNB4 30S ribosomal protein S13 1.52 B5XN86 30S ribosomal protein S7 b a B5XQC8 50S ribosomal protein L35 b a A6TES6 Ribosomal protein L11 methyltransferase b a A6T6T1 Ribosomal protein S12 methylthiotransferase RimO b a A6TEC2 Ribosomal RNA large subunit methyltransferase G b a...”
• Lavender essential oil induces oxidative stress which modifies the bacterial membrane permeability of carbapenemase producing Klebsiella pneumoniae
  Yang, Scientific reports 2020
  • “...Chaperone protein DnaJ dnaJ A6T4F5 Stress response Cytoplasm 3.15398 36 50S ribosomal protein L35 rpmI B5XQC8 Protein biosynthesis Ribosomal protein 3.12775 37 Leucine-responsive regulatory protein lrp P37424 DNA processing Cytoplasm 3.05971 38 Outer membrane protein C ompC Q48473 Transporter protein Membrane 3.03548 39 ATP synthase epsilon...”
• Nonspecific inhibition of Escherichia coli ornithine decarboxylase by various ribosomal proteins: detection of a new ribosomal protein possessing strong antizyme activity.
  Kashiwagi, Biochimica et biophysica acta 1987 (PubMed)
  • GeneRIF: N-terminus verified by Edman degradation on mature peptide
• 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
  • “...STM3430 STM3422 STM4393 STM3441 STM0981 STM3447 STM3448 STM3436 STM3419 STM1335 rplN rplP rpsR rpsJ rpsA rpsG rpsL rpsS rpmJ rpmI 50S 50S 30S 30S 30S 30S 30S...”
• A systems approach discovers the role and characteristics of seven LysR type transcription factors in Escherichia coli
  Rodionova, Scientific reports 2022
  • “...membrane transport protein YnfM 3.06E04 221 1.5 b1656 sodB Superoxide dismutase [Fe] 5.46E05 323 4.8 b1717 rpmI 50S ribosomal protein L35 3.57E05 55 2.4 b1886 tar Methyl-accepting chemotaxis protein II 4.20E05 298 1.4 b1889 motB Motility protein B 3.08E04 61 1.6 b2094 gatA PTS system galactitol-specific...”
• 18th Congress of the European Hematology Association, Stockholm, Sweden, June 13–16, 2013
  , Haematologica 2013
• In vitro transcription profiling of the σS subunit of bacterial RNA polymerase: re-definition of the σS regulon and identification of σS-specific promoter sequence elements
  Maciag, Nucleic acids research 2011
  • “...79 ); upregulated in rpoS mutant of MG1655 ( 17 ) rpmI Ribosomal protein L35 b1717 1.91 prfB Release Factor RF2 b2891 1.91 Upregulated in a biofilm-growing rpoS mutant derivative of MG1655 ( 18 ) rimP Ribosomal maturation protein b3170 2.01 rpsF Ribosomal protein S6 b4200...”
• Analysis of promoter targets for Escherichia coli transcription elongation factor GreA in vivo and in vitro
  Stepanova, Journal of bacteriology 2007
  • “...lpp b1677 1.8 Murein lipoprotein rplT rpmI infC b1716 b1717 Z2747 1.7 1.8 2.0 50S ribosomal subunit protein L20 and regulator 50S ribosomal subunit protein A...”
• Differential gene expression for investigation of Escherichia coli biofilm inhibition by plant extract ursolic acid
  Ren, Applied and environmental microbiology 2005
  • “...0.0220 1.0 0.7185 rmf b0953 1.5 0.0029 1.0 0.6617 rpmI b1717 1.6 0.0072 1.0 0.7076 slp ugpB b3506 b3453 1.5 0.0059 1.6 0.0020 1.4 0.0446 1.5 0.0210 ybiK yhaD...”
• Genome-wide transcriptional profiling of the Escherichia coli responses to superoxide stress and sodium salicylate
  Pomposiello, Journal of bacteriology 2001
  • “...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 atpH...”
• 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 L32 Cytoplasm No Hits 19 NP_709497 50S ribosomal protein L34 Cytoplasm No Hits 20 NP_707397 50S ribosomal protein L35 Cytoplasm No Hits 21 NP_709083 DNA-directed RNA polymerase subunit alpha Cytoplasm No Hits 22 NP_706830 30S ribosomal protein S1 Cytoplasm No Hits 23 NP_708875 30S ribosomal...”
• Global transcriptomic analysis of ethanol tolerance response in Salmonella Enteritidis
  He, Current research in food science 2022
  • “...L2 SEN3256 rplE 3.10 50S ribosomal protein L5 SEN3936 rplL 3.73 50S ribosomal protein L7/L12 SEN1709 rpmI 2.99 50S ribosomal protein L35 SEN0885 rpsA 2.85 30S ribosomal protein S1 SEN3252 rplR 3.90 50S ribosomal protein L18 SEN3261 rplP 3.83 50S ribosomal protein L16 SEN3249 rplO 3.40...”

NGO0297 putative 50s ribosomal protein L35 from Neisseria gonorrhoeae FA 1090
NMB0722 50S ribosomal protein L35 from Neisseria meningitidis MC58
NGFG_00442 50S ribosomal protein L35 from Neisseria gonorrhoeae MS11
44% identity, 94% coverage

• Identification of the iron-responsive genes of Neisseria gonorrhoeae by microarray analysis in defined medium
  Ducey, Journal of bacteriology 2005
  • “...NGO0043c NGO0057 NGO0191 NGO0199c NGO0260 NGO0295 NGO0296 NGO0297 NGO0584 NGO0905 NGO1246c NGO1413 NGO1748c NGO1776 NGO1818c Conserved hypothetical protein 50S...”
• Identification of the iron-responsive genes of Neisseria gonorrhoeae by microarray analysis in defined medium
  Ducey, Journal of bacteriology 2005
  • “...NMB1862 NMB1845 NMB0609 NMB0617 NMB0687 NMB0720 NMB0721 NMB0722 NMB1320 NMB1437 NMB1587 NMB0569 NMB0244 NMB0207 NMB0168 NGO1822c NGO1824.1c NGO1826.1c NGO1828c...”
• Transcriptional landscape and essential genes of Neisseria gonorrhoeae
  Remmele, Nucleic acids research 2014
  • “...sequence 117 bp upstream of a transcript encoding the 50S ribosomal proteins L35 and L20 (NGFG_00442 and NGFG_00443) was exchanged by a Kanamycin-P trc cassette. The P trc promoter is IPTG-inducible as lacI q can bind there as a repressor. In the recombinant strains the expression...”
  • “...show growth defects when IPTG is omitted. These data indicate that the ribosomal protein-encoding genes NGFG_00442 and NGFG_00443 ( P = 0.00061 and 0.00245, respectively) are essential for GC growth (Supplementary Figure S6B). In addition to conditional knockout assays and DNA footprinting analysis, several putative essential...”

Alvin_0982 ribosomal protein L35 from Allochromatium vinosum DSM 180
44% identity, 94% coverage

• Genome-wide transcriptional profiling of the purple sulfur bacterium Allochromatium vinosum DSM 180T during growth on different reduced sulfur compounds
  Weissgerber, Journal of bacteriology 2013
  • “...Alvin_0629 Alvin_0741 Alvin_0742 Alvin_0852 Alvin_0913 Alvin_0982 Alvin_1093 Alvin_1095 Alvin_1196 Alvin_1197 Alvin_1420 Alvin_1436 Alvin_1525 Alvin_1527...”

MT1680 50S ribosomal protein L35 from Mycobacterium tuberculosis CDC1551
Rv1642 50S ribosomal protein L35 from Mycobacterium tuberculosis H37Rv
MRA_1653 50S ribosomal protein L35 from Mycobacterium tuberculosis H37Ra
42% identity, 97% coverage

• Conserved codon composition of ribosomal protein coding genes in Escherichia coli, Mycobacterium tuberculosis and Saccharomyces cerevisiae: lessons from supervised machine learning in functional genomics
  Lin, Nucleic acids research 2002
  • “...MT0736, MT0728, MT0747, MT1337, MT2117.1, MT0663, MT4041.1, MT1680, MT3567.1, MT0729, MT0742, MT0744, MT0681, MT0062 Small subunit 22 MT1666, MT0727, MT3566,...”
• Integrated sequence and -omic features reveal novel small proteome of Mycobacterium tuberculosis
  Sinha, Frontiers in microbiology 2024
  • “...1995 ). In another example, MTB_ORF_16006 is an integral part of an operon comprising Rv1641, Rv1642, Rv1643 , and Rv1644 ( Supplementary Figure 12 ). The proteins in this operon share functions closely related to ribosome assembly and protein synthesis. Notably, MTB_ORF_16006 features a membrane-binding domain...”
  • “...MTB_ORF_54512. Supplementary Figure 12 Representation of MTB_ORF_16006 within an operon that includes the genes Rv1641, Rv1642, Rv1643 , and Rv1644 . Supplementary Table 1 The genomic locations of smORFs and the growth condition in which they were predicted. Supplementary Table 2 The accession numbers and the...”
• Label-Free Comparative Proteomics of Differentially Expressed Mycobacterium tuberculosis Protein in Rifampicin-Related Drug-Resistant Strains
  Ullah, Pathogens (Basel, Switzerland) 2021
  • “...is possibly involved in a transcriptional process, metabolism, and cell development [ 59 ]. RpmI (Rv1642) is an active virulence operon involved in protein synthesis and is associated with invasion and intercellular resistance [ 60 ]. UreA (Rv1848) is involved in the conversion of urea to...”
  • “...PPE19 PE/PPE Rv1534 Rv1534 Possibly involved in a transcriptional mechanism Probable transcriptional regulator Regulatory proteins Rv1642 rpmI Translation 50S ribosomal protein L35 RpmI Information pathways Rv1848 ureA Involved in the conversion of urea to NH 3 [catalytic activity: urea + H 2 O = CO 2...”
• Transcriptional Profile of Mycobacterium tuberculosis in an in vitro Model of Intraocular Tuberculosis
  Abhishek, Frontiers in cellular and infection microbiology 2018
  • “...intracellular replication in ARPE-19 cells. Upregulation of ribosomal ( Rv2056c, Rv3459c, Rv3456c, Rv1630, Rv0720, Rv0979A, Rv1642 , and Rv0700 ), transcriptional ( Rv0823c, Rv1994c, Rv3765c, Rv3160c, Rv1963c, Rv3416, Rv0232, Rv0602c, Rv1129c, Rv2324, Rv3183 , and Rv3833 ), and translation initiation ( Rv3462c ) transcripts whose protein...”
• The effect of growth rate on pyrazinamide activity in Mycobacterium tuberculosis - insights for early bactericidal activity?
  Pullan, BMC infectious diseases 2016
  • “...P41194 30S ribosomal protein S7 4.07 3.05 Rv0718 P66625 30S ribosomal protein S8 3.13 3.04 Rv1642 P66271 50S ribosomal protein L35 2.59 3.02 Rv0714 P66069 50S ribosomal protein L14 2.79 2.92 Rv0707 P0A5X6 30S ribosomal protein S3 1.06 2.91 5S_rRNA ribosomal RNA 2.44 2.91 Rv0721 P66574...”
• Osmosensory signaling in Mycobacterium tuberculosis mediated by a eukaryotic-like Ser/Thr protein kinase
  Hatzios, Proceedings of the National Academy of Sciences of the United States of America 2013
  • “...Rv1072 Rv1078 Rv1297 Rv1462 Rv1463 Rv1464 Rv1466 Rv1641 Rv1642 Rv1643 Rv1652 Rv1653 Rv1654 Rv1655 Rv1656 Rv1657 Rv1658 Rv1659 Rv1886c Rv1908c Rv1980c Rv1996...”
• The Corynebacterium pseudotuberculosis in silico predicted pan-exoproteome
  Santos, BMC genomics 2012
  • “...487 58.67 495 Rv1018c glmU NP_215534.1 bifunctional N-acetylglucosamine-1-phosphate uridyltransferase/glucosamine-1-phosphate acetyltransferase plcpsec115 cpfrc_00945 64 63.33 64 Rv1642 rpmI NP_216158.1 50S ribosomal protein L35 plcppse080 cpfrc_01015 452 57.08 470 Rv0392c ndhA NP_214906.1 membrane NADH dehydrogenase plcppse080 cpfrc_01015 452 58.10 463 Rv1854c ndh NP_216370.1 NADH dehydrogenase plcpsec041 cpfrc_01074 403...”
• 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
  • “...2.0 Annotationb or similarityc to protein domains Rv1594 Rv1596 Rv1623c Rv1642 Rv1653 Rv1687c 1.4 1.3 0.9 1.0 1.3 1.0 0.6 1.7 0.6 1.6 1.6 0.6 1.0 1.0 0.9 1.4...”
• The gene expression data of Mycobacterium tuberculosis based on Affymetrix gene chips provide insight into regulatory and hypothetical genes
  Fu, BMC microbiology 2007
  • “...rplD 4868 415 Rv2159c - 3197 832 Rv0701 rplC 4822 429 Rv0640 rplK 3169 256 Rv1642 rpmI 4816 562 Rv2392 cysH 3147 663 Rv2244 acpM 4650 1053 Rv2196 qcrB 3137 578 Rv1884c rpfC 4642 615 Rv2391 nirA 3110 822 Rv1305 atpE 4488 679 Rv0289 - 3088...”
• More
• 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_001283215.1 Secreted antigen 85-B FbpB Up Down Up MRA_1706 YP_001283017.1 Hypothetical protein Up Up Up MRA_1653 YP_001282961.1 50S ribosomal protein L35 Up Up Up MRA_1624 YP_001282932.1 Prolipoprotein diacylglyceryl transferase Up Up Up MRA_1622 YP_001282930.1 Tryptophan synthase subunit beta Up Up Up MRA_1323 YP_001282626.1 UDP- N -acetylglucosamine...”

B0JSJ9 Large ribosomal subunit protein bL35 from Microcystis aeruginosa (strain NIES-843 / IAM M-2473)
43% identity, 97% coverage

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

PD1914 50S ribosomal protein L35 from Xylella fastidiosa Temecula1
46% identity, 98% coverage

• Csp1, a Cold Shock Protein Homolog in Xylella fastidiosa Influences Cell Attachment, Pili Formation, and Gene Expression
  Wei, Microbiology spectrum 2021
  • “...PD1440 rpsT 30S ribosomal protein S20 6,060.28 1,246.99 0.21 PD0708 Virulence regulator 672.31 141.02 0.21 PD1914 rpmI 50S ribosomal protein L35 21,603.77 4,619.53 0.21 PD0626 ssb Single-stranded DNA-binding protein 484.98 103.71 0.21 PD0061 fimC Chaperone protein precursor 477.40 108.95 0.23 PD1087 Hypothetical protein 2,361.29 585.51 0.25...”

8a3l2 / P0A7Q1 8a3l2 (see paper)
46% identity, 92% coverage

• Ligand: rna (8a3l2)

MSMEG_3792, MSMEI_3704 50S ribosomal protein L35 from Mycolicibacterium smegmatis MC2 155
A0QYU7 Large ribosomal subunit protein bL35 from Mycolicibacterium smegmatis (strain ATCC 700084 / mc(2)155)
MSMEG_3792 ribosomal protein L35 from Mycobacterium smegmatis str. MC2 155
42% identity, 97% coverage

• Interactome Analysis Identifies MSMEI_3879 as a Substrate of Mycolicibacterium smegmatis ClpC1
  Ogbonna, Microbiology spectrum 2023
  • “...0.01 A0QSG0 rplX , MSMEG_1466, MSMEI_1430 50S ribosomal protein L24 0.02 0.02 A0QYU7 rpmI , MSMEG_3792, MSMEI_3704 50S ribosomal protein L35 0.01 0.01 A0QSP8 rplM , MSMEG_1556, MSMEI_1519 50S ribosomal protein L13 0.08 0.07 A0QSD2 rplD , MSMEG_1437, MSMEI_1401 50S ribosomal protein L4 0.05 0.07 A0QSG6...”
  • “...A0QSG0 rplX , MSMEG_1466, MSMEI_1430 50S ribosomal protein L24 0.02 0.02 A0QYU7 rpmI , MSMEG_3792, MSMEI_3704 50S ribosomal protein L35 0.01 0.01 A0QSP8 rplM , MSMEG_1556, MSMEI_1519 50S ribosomal protein L13 0.08 0.07 A0QSD2 rplD , MSMEG_1437, MSMEI_1401 50S ribosomal protein L4 0.05 0.07 A0QSG6 rpsE...”
• Interactome Analysis Identifies MSMEI_3879 as a Substrate of Mycolicibacterium smegmatis ClpC1
  Ogbonna, Microbiology spectrum 2023
  • “...protein L22 0.03 0.01 A0QSG0 rplX , MSMEG_1466, MSMEI_1430 50S ribosomal protein L24 0.02 0.02 A0QYU7 rpmI , MSMEG_3792, MSMEI_3704 50S ribosomal protein L35 0.01 0.01 A0QSP8 rplM , MSMEG_1556, MSMEI_1519 50S ribosomal protein L13 0.08 0.07 A0QSD2 rplD , MSMEG_1437, MSMEI_1401 50S ribosomal protein L4...”
• Gene Expression, Bacteria Viability and Survivability Following Spray Drying of Mycobacterium smegmatis
  Lauten, Materials (Basel, Switzerland) 2010
  • “...L33 rpmG 0.6 11.6 0.045 9% MSMEG_6946 ribosomal protein L34 rpmH 0.3 11.5 0.282 0% MSMEG_3792 ribosomal protein L35 rpmI 0.8 13.6 0.004 46% MSMEG_1520 ribosomal protein L36 rpmJ 0.4 13.3 0.080 1% MSMEG_3833 ribosomal protein S1 -0.3 12.1 0.174 1% MSMEG_2519 ribosomal protein S2 rpsB...”

CT834 L35 Ribosomal Protein from Chlamydia trachomatis D/UW-3/CX
40% identity, 94% coverage

• Simultaneous transcriptional profiling of bacteria and their host cells
  Humphrys, PloS one 2013
  • “...assays were designed for genes CT81, CT500, CT229, CT875, CT734, CT446, CT577, CT18, CT864, CT665, CT834, CT391, CT216, CT705, and CT416. Chlamydial gene expression is plotted against the RPKM for each gene. qRT-PCR data is expressed as 1/log2 Ct and normalized to 16S rRNA. (PDF) Click...”

ssl1426 50S ribosomal protein L35 from Synechocystis sp. PCC 6803
42% identity, 93% coverage

• Proteomic analysis of the regulatory networks of ClpX in a model cyanobacterium Synechocystis sp. PCC 6803
  Zhang, Frontiers in plant science 2022
  • “...large subunit), including rplB (sll1802), rplX (sll1807), rpsK (sll1817), rplT (sll0767), rpsL (sll1096), and rpmI (ssl1426). Furthermore, many proteases, such as hhoA (sll1679), ymxG (slr1331), htrA (slr1204), methionine aminopeptidase (sll0555), and putative carboxypeptidase (sll0777), were significantly upregulated. As mentioned above, ClpX functions as a chaperone for...”
  • “...from 50S ribosomal protein L2 (sll1802), 50S ribosomal protein L24 (sll1807), 50S ribosomal protein L35 (ssl1426), and 30S ribosomal protein S11 (sll1817) are shown in Figure5C . Figure5 Validation of DEPs using Parallel Reaction Monitoring (PRM) analysis. (A) Pairwise correlation of peak area of transitions for...”
• A transcriptional regulator Sll0794 regulates tolerance to biofuel ethanol in photosynthetic Synechocystis sp. PCC 6803
  Song, Molecular & cellular proteomics : MCP 2014
  • “...Slr1597 Slr1727 Slr1838 Slr1856 Slr1974 Slr2041 Slr2059 Ssl1426 Ssl1784 Ssl3044 Ssl3432 Ssl3441 Ssl3445 Ssr0482 Ssr1604 Ssr2799 Mutant_r1 vs. Control_r1...”
• Proteomic analysis reveals resistance mechanism against biofuel hexane in Synechocystis sp. PCC 6803
  Liu, Biotechnology for biofuels 2012
  • “...Sll1813 1.60 50S ribosomal protein L15 Ssl3436 2.58 2.06 1.72 1.71 50S ribosomal protein L29 Ssl1426 2.07 50S ribosomal protein L35 Ssl2084 3.11 3.46 3.55 5.13 1.95 Acyl carrier protein Sll1017 1.93 Ammonium/methylammonium permease Slr0242 1.58 1.66 Bacterioferritin co migratory protein Slr0043 2.56 Bicarbonate transport system...”
• RNA-seq based identification and mutant validation of gene targets related to ethanol resistance in cyanobacterial Synechocystis sp. PCC 6803
  Wang, Biotechnology for biofuels 2012
  • “...4.12E+05 6.41E+05 9.77E+05 1.72E+05 3.12E+05 5.68E+05 2.51E+05 6.14E+05 5.94E+05 50S ribosomal protein L24 Protein synthesis ssl1426 5.89E+06 2.35E+06 5.49E+06 4.31E+06 4.18E+06 2.74E+06 2.30E+06 2.22E+06 2.17E+06 50S ribosomal protein L35 Protein synthesis slr2067 1.00E+06 2.39E+06 4.47E+06 3.52E+05 1.16E+06 2.61E+06 8.80E+05 3.28E+06 3.45E+06 Allophycocyanin alpha subunit Energy metabolism...”
• Gene expression patterns of sulfur starvation in Synechocystis sp. PCC 6803
  Zhang, BMC genomics 2008
  • “...( rpl5 ), sll1809 ( rps8 ), sll1810 ( rpl6 ), sll1813 ( rpl15 ), ssl1426 ( rpl35 )) 13 RNA polymerase subunits (sll1787( rpoB ), sll1789( rpoC2 ), sll1818( rpoA )), Translation (sll1820( truA ), sll1099( tufA ), Ribosomal proteins (sll0767( rpl20 ), sll1745( rpl10...”

Q9Z6R8 Large ribosomal subunit protein bL35 from Chlamydia pneumoniae
39% identity, 94% coverage

• Prediction of Chlamydia pneumoniae protein localization in host mitochondria and cytoplasm and possible involvements in lung cancer etiology: a computational approach
  Alshamsan, Saudi pharmaceutical journal : SPJ : the official publication of the Saudi Pharmaceutical Society 2017
  • “...(Q9Z6V3), L4 (Q9Z7Q8), L5 (Q9Z7R9), L29 (Q9Z7R5), L27 (Q9Z807), L33 (Q9Z8T4), L34 (Q9Z6X1) and L35 (Q9Z6R8), L36 (Q9Z6X0), which potentially involved in various steps of translation and ribosome biogenesis in C. pneumoniae . Control of translation is a critical component for the progress and advancement of...”

PA2742 50S ribosomal protein L35 from Pseudomonas aeruginosa PAO1
Q9I0A1 Large ribosomal subunit protein bL35 from Pseudomonas aeruginosa (strain ATCC 15692 / DSM 22644 / CIP 104116 / JCM 14847 / LMG 12228 / 1C / PRS 101 / PAO1)
44% identity, 94% coverage

• The AraC-Type Transcriptional Regulator GliR (PA3027) Activates Genes of Glycerolipid Metabolism in Pseudomonas aeruginosa
  Kotecka, International journal of molecular sciences 2021
  • “...universal stress protein 11 intra 09845 PA3083 1.51 8.26 2,055,622 TPTMD aminopeptidase 12 intra 11,685 PA2742 1.20 3.10 2,411,617 TPTMD 50S ribosomal protein L35 13 prom 12,415 PA2601 1.04 3.90 2,570,649 TR LysR family transcriptional regulator 12,420 PA2602 1.75 HUU 3-mercaptopropionate dioxygenase 14 term 12,415 PA2601...”
• Proteomic Analysis of Vesicle-Producing Pseudomonas aeruginosa PAO1 Exposed to X-Ray Irradiation
  Zhang, Frontiers in microbiology 2020
  • “...PA2562 1.591 0.703 2.2562 Uncharacterized protein Q9I0H1 PA2667 MvaU 1.832 0.713 2.569 Uncharacterized protein Q9I0A1 PA2742 RpmI 1.243 0.179 6.944 50S ribosomal protein L35 Q9HZZ0 PA2854 1.662 0.608 2.73 Uncharacterized protein Q00514 PA3101 XcpT 1.293 0.567 2.28 Type II secretion system protein G Q9HZ35 PA3205 1.249...”
• The Pseudomonas aeruginosa CreBC two-component system plays a major role in the response to β-lactams, fitness, biofilm growth, and global regulation
  Zamorano, Antimicrobial agents and chemotherapy 2014
  • “...PA0519 PA0523 PA0524 PA0525 PA0918 PA1557 PA1582 PA1588 PA2742 PA3205 PA3392 PA3393 PA3394 PA3395 PA3872 PA3873 PA3874 PA3875 PA3876 PA3877 PA3915 PA4110 PA4238...”
• Proteomic Analysis of Vesicle-Producing Pseudomonas aeruginosa PAO1 Exposed to X-Ray Irradiation
  Zhang, Frontiers in microbiology 2020
  • “...Q9I0S3 PA2562 1.591 0.703 2.2562 Uncharacterized protein Q9I0H1 PA2667 MvaU 1.832 0.713 2.569 Uncharacterized protein Q9I0A1 PA2742 RpmI 1.243 0.179 6.944 50S ribosomal protein L35 Q9HZZ0 PA2854 1.662 0.608 2.73 Uncharacterized protein Q00514 PA3101 XcpT 1.293 0.567 2.28 Type II secretion system protein G Q9HZ35 PA3205...”
• Top-Down LESA Mass Spectrometry Protein Analysis of Gram-Positive and Gram-Negative Bacteria
  Kocurek, Journal of the American Society for Mass Spectrometry 2017
  • “...L33 Q9HTN9 31 Incubation and storage: 4 days, room temperature 723.8214 +10 7228.14 -2.0 L35 Q9I0A1 41 -Met 739.5860 +6 4431.47 -1.2 L36 Q9HWF6 45 759.9734 +11 8348.63 -1.4 S21 Q9I5V8 29 -Met 826.5565 +11 9081.04 -0.3 HU- P05384 51 Incubation: 48 h, 37 C Sampled...”

7f0d3 / A5U2Z9 Cryo-em structure of mycobacterium tuberculosis 50s ribosome subunit bound with clarithromycin (see paper)
41% identity, 92% coverage

• Ligand: rna (7f0d3)

Rmet_1162 50S ribosomal protein L35 from Cupriavidus metallidurans CH34
37% identity, 94% coverage

• Importance of RpoD- and Non-RpoD-Dependent Expression of Horizontally Acquired Genes in Cupriavidus metallidurans
  Große, Microbiology spectrum 2022
  • “...thrS 12.4 714 37 TTGCGTAACG 16 TATAAAATTC Rmet_1161 infC 10.8 2,673 36 TTGATAACGA 13 GTCAAATTCA Rmet_1162 rpmI 11.4 68 35 TTGCGTTCCG 14 AAGATACTGG Rmet_1166 ihfA 10.6 245 39 TTTGTTTGCG 15 GCTATAATTG Rmet_1975 dnaB 6.9 49 35 TTGCGGGAAG 13 GCTATACTCG Rmet_1979 rpsF 12.2 1,413 36 TGGAAAGCCT 15...”

Q67W51 50S ribosomal protein L35 from Oryza sativa subsp. japonica
42% identity, 44% coverage

• Carbon and nitrogen partitioning of transgenic rice T2A-1 (Cry2A*) with different nitrogen treatments
  Ling, Scientific reports 2019
  • “...1 0.733 0.012 Uncharacterized protein B9FFK4 5.32 1 1 0.736 0.014 50S ribosomal protein L35 Q67W51 4.11 1 1 0.748 0.019 Os01g0717000 protein (Fragment) A0A0P0V7D0 9.09 1 1 0.751 0.020 ATP-dependent 6-phosphofructokinase A2ZQ69 12.33 1 5 0.757 0.024 Glutathione peroxidase B7FAE9 30.34 1 6 0.765 0.030...”

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Statistics

How It Works

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

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

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

PaperBLAST also incorporates manually-curated protein functions:

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

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

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

Changes to PaperBLAST since the paper was written:

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

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

Secrets

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

Omissions from the PaperBLAST Database

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

References

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

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

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

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

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

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

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

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

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

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

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

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