PaperBLAST

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

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>59 a.a. (MKVKSAAKKR...)
MKVKSAAKKRFKLTKSGQIKRKHAYTSHLAPHKTTKQKRHLRKQGTVSASDFKRIGNLI

Running BLASTp...

Found 29 similar proteins in the literature:

7ood1 / P75447 Mycoplasma pneumoniae 50s subunit of ribosomes in chloramphenicol- treated cells (see paper)
MPN116 ribosomal protein L35 from Mycoplasma pneumoniae M129
100% identity, 100% 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...”

MHO_1280 50S ribosomal protein L35 from Mycoplasma hominis
61% identity, 95% 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...”

GBAA_4818 50S ribosomal protein L35 from Bacillus anthracis str. 'Ames Ancestor'
63% identity, 82% 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...”

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
58% identity, 89% coverage

• subunit: Part of the 50S ribosomal subunit.
• 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...”
• 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...”

8buu3 / P55874 8buu3 (see paper)
58% identity, 91% coverage

• Ligand: rna (8buu3)

8uu97 / A0A660JIB9 8uu97 (see paper)
53% identity, 91% coverage

• Ligand: rna (8uu97)

lmo1784 ribosomal protein L35 from Listeria monocytogenes EGD-e
Q71YN4 Large ribosomal subunit protein bL35 from Listeria monocytogenes serotype 4b (strain F2365)
53% identity, 89% coverage

• 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...”
• 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...”

EKM74_RS01860 50S ribosomal protein L35 from Staphylococcus aureus
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
SACOL1726 ribosomal protein L35 from Staphylococcus aureus subsp. aureus COL
56% identity, 89% coverage

• 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...”
• 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...”
• 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...”

5nrg3 / Q2FXQ0 The crystal structure of the large ribosomal subunit of staphylococcus aureus in complex with rb02 (see paper)
56% identity, 91% coverage

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

A4VVU6 Large ribosomal subunit protein bL35 from Streptococcus suis (strain 05ZYH33)
SSU05_1269 50S ribosomal protein L35 from Streptococcus suis 05ZYH33
57% identity, 88% 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...”

D0R5D2 Large ribosomal subunit protein bL35 from Lactobacillus johnsonii (strain FI9785)
55% identity, 88% 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...”

SPy0805 50S ribosomal protein L35 from Streptococcus pyogenes M1 GAS
57% identity, 83% 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)
56% identity, 82% 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...”

azo1081 50S ribosomal protein L35 from Azoarcus sp. BH72
53% identity, 91% 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...”

spr0862 50S Ribosomal protein L35 from Streptococcus pneumoniae R6
52% identity, 88% 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...”

NMB0722 50S ribosomal protein L35 from Neisseria meningitidis MC58
NGO0297 putative 50s ribosomal protein L35 from Neisseria gonorrhoeae FA 1090
NGFG_00442 50S ribosomal protein L35 from Neisseria gonorrhoeae MS11
44% identity, 91% coverage

• 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...”
• 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...”
• 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...”

sync_0059 ribosomal protein L35 from Synechococcus sp. CC9311
42% identity, 91% 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...”

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
49% identity, 91% 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...”

5myjB7 / A2RMR2 of 70S ribosome from Lactococcus lactis (see paper)
52% identity, 84% coverage

• Ligand: rna (5myjB7)

SYNW0058 50S ribosomal protein L35 from Synechococcus sp. WH 8102
42% identity, 91% 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...”

BB0189 ribosomal protein L35 (rpmI) from Borrelia burgdorferi B31
41% identity, 89% coverage

• Norepinephrine mediates acquisition of transferrin-iron in Bordetella bronchiseptica
  Anderson, Journal of bacteriology 2008
  • “...February 16, 2017 by University of California, Berkeley BB0189 J. BACTERIOL. VOL. 190, 2008 NOREPINEPHRINE-MEDIATED IRON ACQUISITION 3943 FIG. 1. Analysis of...”
  • “...present study, three additional putative TonB-dependent receptors (BB0189, BB2179, and BB4457) were identified in the B. bronchiseptica genome sequence, based...”

MSMEG_3792 ribosomal protein L35 from Mycobacterium smegmatis str. MC2 155
A0QYU7 Large ribosomal subunit protein bL35 from Mycolicibacterium smegmatis (strain ATCC 700084 / mc(2)155)
MSMEG_3792, MSMEI_3704 50S ribosomal protein L35 from Mycolicibacterium smegmatis MC2 155
47% identity, 91% 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...”
• 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...”
• 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...”
• Interactome Analysis Identifies MSMEI_3879 as a Substrate of Mycolicibacterium smegmatis ClpC1
  Ogbonna, Microbiology spectrum 2023
  • “...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...”

PD1914 50S ribosomal protein L35 from Xylella fastidiosa Temecula1
44% identity, 91% 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...”

SG1420 50S ribosomal protein L35 from Sodalis glossinidius str. 'morsitans'
50% identity, 80% 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)...”

lpp2768 50S ribosomal protein L35 from Legionella pneumophila str. Paris
50% identity, 77% 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...”

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)
49% identity, 86% 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...”
• Proteome-wide identification of druggable targets and inhibitors for multidrug-resistant <i>Pseudomonas aeruginosa</i> using an integrative subtractive proteomics and virtual screening approach
  Vemula, Heliyon 2025
  • “...5022 Q9I6Q6 695 Q9HWX5 1777 Q9I0A0 2859 Q9HVX5 3941 Q9I111 5023 Q9I6Q7 696 Q9HWX7 1778 Q9I0A1 2860 Q9HVX8 3942 Q9I112 5024 Q9I6Q9 697 Q9HWY1 1779 Q9I0A2 2861 Q9HVX9 3943 Q9I113 5025 Q9I6R3 698 Q9HWZ6 1780 Q9I0A7 2862 Q9HVY1 3944 Q9I115 5026 Q9I6R4 699 Q9HX02 1781 Q9I0B0...”
• 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...”

8cd15 / Q9I0A1 8cd15 (see paper)
49% identity, 87% coverage

• Ligand: rna (8cd15)

ISORED2_02500 50S ribosomal protein L35 from Acetobacterium wieringae
42% identity, 88% 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...”

BPSL1943 50S ribosomal protein L35 from Burkholderia pseudomallei K96243
BTH_I2593 ribosomal protein L35 from Burkholderia thailandensis E264
bglu_1g21500 Ribosomal protein L35 from Burkholderia glumae BGR1
41% identity, 91% coverage

• Unraveling the role of toxin-antitoxin systems in Burkholderia pseudomallei: exploring bacterial pathogenesis and interactions within the HigBA families
  Chapartegui-González, Microbiology spectrum 2024
  • “...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...”
• 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 (...”
• 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...”

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.