PaperBLAST

PaperBLAST Hits for LRK54_RS03535 (61 a.a., MASKDINNQS...)

Show query sequence

>LRK54_RS03535
MASKDINNQSAEELQQHLLDLRKEQFNLRMQKGSGQLTQPHQLRRVRRDIARTKFVLGGK
K

Running BLASTp...

Found 43 similar proteins in the literature:

Q5GWU2 Large ribosomal subunit protein uL29 from Xanthomonas oryzae pv. oryzae (strain KACC10331 / KXO85)
57% identity, 100% coverage

• Antibacterial Activities and Underlying Mechanisms of the Compound SYAUP-491 against Xanthomonas oryzae pv. oryzae
  Li, Molecules (Basel, Switzerland) 2024
  • “...L2 xoo:XOO3580 0.635694 0.018403 RL32_XANOR Q05I49 rpmF 50S ribosomal protein L32 xoo:XOO4732 0.701572 0.036503 RL29_XANOR Q5GWU2 rpmC 50S ribosomal protein L29 xoo:XOO3575 0.446445 0.001933 RL34_XANOR Q05HP6 rpmH 50S ribosomal protein L34 xoo:XOO4957 0.121112 0.003118 RL33_XANOR Q5GU11 rpmG 50S ribosomal protein L33 xoo:XOO4558 0.101754 0.000052...”

VP0265 ribosomal protein L29 from Vibrio parahaemolyticus RIMD 2210633
55% identity, 95% coverage

• Insights into Vibrio parahaemolyticus CHN25 response to artificial gastric fluid stress by transcriptomic analysis
  Sun, International journal of molecular sciences 2014
  • “...5.5738 50S ribosomal protein L27 VP0185 ( rpmB ) Chn25_0181 2.7392 50S ribosomal protein L28 VP0265 ( rpmC ) Chn25_0256 2.5323 50S ribosomal protein L29 VP0255 ( rpmE ) Chn25_0246 5.0193 50S ribosomal protein L31 VP0186 ( rpmG ) Chn25_0182 7.2192 50S ribosomal protein L33 VP2030...”
• Rapid identification of Vibrio parahaemolyticus by whole-cell matrix-assisted laser desorption ionization-time of flight mass spectrometry
  Hazen, Applied and environmental microbiology 2009
  • “...protein 50S ribosomal protein L17 VP0275 VP2529 VP0265 VP2335 VP2817 VP2331 VP0160 VP1210 VP0261 VPA0321 VPA0286 VP2627 VP2619 VP2029 VPA0577 VP2530...”

VDA_003447 50S ribosomal protein L29 from Photobacterium damselae subsp. damselae CIP 102761
55% identity, 95% coverage

• Transcriptome changes in response to temperature in the fish pathogen Photobacterium damselae subsp. damselae: Clues to understand the emergence of disease outbreaks at increased seawater temperatures
  Matanza, PloS one 2018
  • “...shock protein 12798 VDA_001583 NAD-dependent glyceraldehyde-3-phosphate dehydrogenase 12190 VDA_003449 LSU ribosomal protein L14p (L23e) 11923 VDA_003447 LSU ribosomal protein L29p (L35e) 11833 VDA_003446 LSU ribosomal protein L16p (L10e) 11690 VDA_000159 Damselysin toxin (Dly) 10938 VDA_003456 SSU ribosomal protein S5p (S2e) 10255 10.1371/journal.pone.0210118.t004 Table 4 List of...”
  • “...the three biological replicates. Locus tag Protein FPKM VDA_003450 LSU ribosomal protein L24p (L26e) 16486 VDA_003447 LSU ribosomal protein L29p (L35e) 15622 VDA_003093 LSU ribosomal protein L7/L12 (L23e) 15513 VDA_003446 LSU ribosomal protein L16p (L10e) 14870 VDA_003461 SSU ribosomal protein S13p (S18e) 13609 VDA_003444 LSU ribosomal...”

SO0239 ribosomal protein L29 from Shewanella oneidensis MR-1
53% identity, 95% coverage

• Transcriptome analysis reveals a stress response of Shewanella oneidensis deprived of background levels of ionizing radiation
  Castillo, PloS one 2018
  • “...protein L22 -1.07 SO0237 rpsC Ribosomal protein S3 -1.03 SO0238 rplP Ribosomal protein L16 -1.12 SO0239 rpmC Ribosomal protein L29 -1.45 SO0240 rpsQ Ribosomal protein S17 -1.47 -1.06 SO0241 rplN Ribosomal protein L14 -1.24 SO0244 rpsN Ribosomal protein S14 -1.09 SO0247 rplR Ribosomal protein L18 -1.20...”
• Phenotypic Characterisation of Shewanella oneidensis MR-1 Exposed to X-Radiation
  Brown, PloS one 2015
  • “...SO3426). 7170 71687173 + 7170 Da 50S ribosomal protein L29 (rpmC) inferred from homology (Locus SO0239). 7269 72667274 + 7269 Da uncharacterised protein (predicted; Locus SO0886); 7263 Da Molybdenum-pterin binding protein (MopI) (predicted; Locus SO1799). 7393 73927393 - 7392 Da uncharacterised protein (predicted; Locus SO3548). 7603...”

WP_038089319 50S ribosomal protein L29 from Acidihalobacter prosperus
53% identity, 85% coverage

• Multiple Osmotic Stress Responses in Acidihalobacter prosperus Result in Tolerance to Chloride Ions
  Dopson, Frontiers in microbiology 2016
  • “...protein 9.7 2.3 WP_038087805 ATP synthase subunit b 8.2 3.5 WP_038092630 SirA-like protein 6.6 3.3 WP_038089319 50S ribosomal protein L29 3.8 0.4 WP_038088471 Sulfur oxidation protein, SoxZ 2.9 0.3 UP-REGULATED IN LOW SALT CONDITIONS Osmoregulation WP_052064171 OmpA 0.5 0.3 WP_038092666 Protein AsmA 0.3 0.1 Cell Envelope...”

NMA0121 50S ribosomal protein L29 from Neisseria meningitidis Z2491
NMB0150 50S ribosomal protein L29 from Neisseria meningitidis MC58
NGO1831 putative 50S ribosomal subunit protein L29 from Neisseria gonorrhoeae FA 1090
54% identity, 90% coverage

• Transcriptome analysis of Neisseria meningitidis during infection
  Dietrich, Journal of bacteriology 2003
  • “...NMA1964 NMA0612 NMA0600/NMA1174 NMA0128 NMA0127 NMA0123 NMA0122 NMA0121 NMA0120 NMA0112 NMA0111 NMA0110 NMA0108 NMA0107 NMA0104 NMA0102 NMA1137 NMA1138 NMA0027...”
• Transcriptome analysis of Neisseria meningitidis during infection
  Dietrich, Journal of bacteriology 2003
  • “...NMB1710 NMB1845 NMB1857/NMB0977 NMB0143 NMB0144 NMB0148 NMB0149 NMB0150 NMB0151 NMB0159 NMB0160 NMB0161 NMB0163 NMB0164 NMB0167 NMB0169 NMB0941 NMB0942 NMB0232...”
• Global Network Analysis of Neisseria gonorrhoeae Identifies Coordination between Pathways, Processes, and Regulators Expressed during Human Infection
  McClure, mSystems 2020
  • “...0.000 NGO1809 Genetic information processing Carbohydrate metabolism 0.001 NGO1823 Genetic information processing Carbohydrate metabolism 0.013 NGO1831 Genetic information processing Carbohydrate metabolism 0.005 NGO1836 Genetic information processing Energy metabolism 0.006 NGO2030 Energy metabolism Cellular processes/organismal systems/human disease 0.015 NGO2148 Energy metabolism Genetic information processing 0.004 NGO2151 Energy...”
• RpoH mediates the expression of some, but not all, genes induced in Neisseria gonorrhoeae adherent to epithelial cells
  Du, Infection and immunity 2006
  • “...NGO1366 NGO1291 NGO0199 NGO1515 NGO1493 NGO1439 NGO0989 NGO1831 NGO1841 NGO1668 NGO0637 NGO1773 NGO2180 NGO0962 NGO5041 NGO1587 NGO0276 rpoH groES groEL ppiB...”

HI0785 ribosomal protein L29 (rpL29) from Haemophilus influenzae Rd KW20
53% identity, 95% coverage

• Initial proteome analysis of model microorganism Haemophilus influenzae strain Rd KW20
  Kolker, Journal of bacteriology 2003
  • “...HI0201 HI1320 HI0880 HI0782 HI0779 HI0789 HI1630 HI0879 HI0951 HI0785 HI0796 HI0758 HI0158 HI0950 HI0998 HI1319m HI0798.1 550 252 236 207 167 131 157 131 131...”
• Gene expression changes triggered by exposure of Haemophilus influenzae to novobiocin or ciprofloxacin: combined transcription and translation analysis
  Gmuender, Genome research 2001
  • “...hi0921 hi0718 hi0689 hi0768 hi0624 hi0600 hi0567 hi1220 hi0785 hi0516 hi0782 hi0779 hi0571 hi0150 36 Genome Research www.genome.org Gene product 10 min 60 min...”

PD0445 50S ribosomal protein L29 from Xylella fastidiosa Temecula1
51% identity, 78% coverage

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

Psyr_4540 Ribosomal protein L29 from Pseudomonas syringae pv. syringae B728a
53% identity, 90% coverage

• Involvement of rppH in thermoregulation in Pseudomonas syringae
  Hockett, Journal of bacteriology 2014
  • “...Translation Psyr_4525 Psyr_4526 Psyr_4538 Psyr_4539 Psyr_4540 Psyr_4541 Psyr_4542 Psyr_4543 Psyr_4544 Psyr_4545 Psyr_4546 Psyr_4547 Psyr_4548 Psyr_4550...”

Q9HWE3 Large ribosomal subunit protein uL29 from Pseudomonas aeruginosa (strain ATCC 15692 / DSM 22644 / CIP 104116 / JCM 14847 / LMG 12228 / 1C / PRS 101 / PAO1)
PA4255 50S ribosomal protein L29 from Pseudomonas aeruginosa PAO1
53% identity, 90% coverage

• 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
  • “...4730 Q9I5F4 403 P05695 1485 Q9HWE2 2567 Q9HU98 3649 Q9HZR5 4731 Q9I5F8 404 P07344 1486 Q9HWE3 2568 Q9HUA0 3650 Q9HZR7 4732 Q9I5G0 405 P08280 1487 Q9HWE4 2569 Q9HUA1 3651 Q9HZR8 4733 Q9I5G1 406 P0DP44 1488 Q9HWE5 2570 Q9HUA2 3652 Q9HZR9 4734 Q9I5G2 407 P10932 1489 Q9HWE6...”
• Proteomic profiling spotlights the molecular targets and the impact of the natural antivirulent umbelliferone on stress response, virulence factors, and the quorum sensing network of Pseudomonas aeruginosa
  Kasthuri, Frontiers in cellular and infection microbiology 2022
  • “...Q9HVL6 50S ribosomal protein L21 RplU 0.020 1.928 Q9HZZ2 Elongation factor P Efp 0.021 2.674 Q9HWE3 50S ribosomal protein L29 RpmC 0.033 26.692 Q9HV46 Transcription elongation factor GreA 0.034 1.478 Q9HWE9 30S ribosomal protein S8 RpsH 0.040 3.023 Q9HT16 ATP synthase subunit b AtpF 0.050 1.469...”
• Proteomic Analysis of Vesicle-Producing Pseudomonas aeruginosa PAO1 Exposed to X-Ray Irradiation
  Zhang, Frontiers in microbiology 2020
  • “...2.86 Probable DNA binding protein Q9HWE8 PA4250 RpsN 0.911 0.395 2.306 30S ribosomal protein S14 Q9HWE3 PA4255 RpmC 1.86 0.28 3.496 50S ribosomal protein L29 G3XD15 PA4552 PilW 1.242 0.586 2.12 Type 4 fimbrial biogenesis protein Q9HVA8 PA4687 HitA 1.679 0.587 2.86 Ferric iron-binding periplasmic protein...”
• Top-Down LESA Mass Spectrometry Protein Analysis of Gram-Positive and Gram-Negative Bacteria
  Kocurek, Journal of the American Society for Mass Spectrometry 2017
  • “...996.4895 +14 13,936.75 -0.8 Azurin P00282 14 -signal peptide, disulfide 1029.1389 +7 7196.92 -0.6 L29 Q9HWE3 29 Incubation: 48 h, 37 C Sampled fresh 1090.1381 +5 5445.65 0.4 PA2146 Q9I1W9 67 -Met 1223.5075 +7 8557.50 -0.7 PA4739 Q9HV60 61 -signal peptide (132) 1245.9733 +6 7469.80 -0.2...”
• Distinct transcriptome and traits of freshly dispersed Pseudomonas aeruginosa cells
  Kalia, mSphere 2024
  • “...0.966522 PA4248 Upregulated 1.036283 Upregulated 0.702379 PA4249 rpsH-30S ribosomal protein S8 Upregulated 1.439878 Upregulated 1.194785 PA4255 rpmC-50S ribosomal protein L29 Upregulated 0.987271 Upregulated 0.700314 PA4256 rpIP-50S ribosomal protein L16 Upregulated 1.448582 Upregulated 1.059879 PA4261 rpIW-50S ribosomal protein L23 Upregulated 1.18652 Upregulated 0.891766 PA4266 fusA1-elongation factor G...”
• Full Transcriptomic Response of Pseudomonas aeruginosa to an Inulin-Derived Fructooligosaccharide
  Rubio-Gómez, Frontiers in microbiology 2020
  • “...chain release factor 3 0.9 0.000 0.7 0.001 PA3990 Uncharacterized protein 1.3 0.000 0.9 0.000 PA4255 rpmC 50S ribosomal protein L29 0.9 0.000 0.8 0.000 PA4264 rpsJ 30S ribosomal protein S10 0.7 0.001 0.6 0.004 PA4270 rpoB DNA-directed RNA polymerase beta chain 0.4 0.009 0.5 0.003...”
  • “...0.004 PA3903 prfC Peptide chain release factor 3 0.7 0.001 PA3990 Uncharacterized protein 0.9 0.000 PA4255 rpmC 50S ribosomal protein L29 1.1 0.000 PA4264 rpsJ 30S ribosomal protein S10 0.8 0.000 PA4270 rpoB DNA-directed RNA polymerase beta chain 0.9 0.000 PA4280 birA Regulation of transcription 0.6...”
• Proteomic Analysis of Vesicle-Producing Pseudomonas aeruginosa PAO1 Exposed to X-Ray Irradiation
  Zhang, Frontiers in microbiology 2020
  • “...Probable DNA binding protein Q9HWE8 PA4250 RpsN 0.911 0.395 2.306 30S ribosomal protein S14 Q9HWE3 PA4255 RpmC 1.86 0.28 3.496 50S ribosomal protein L29 G3XD15 PA4552 PilW 1.242 0.586 2.12 Type 4 fimbrial biogenesis protein Q9HVA8 PA4687 HitA 1.679 0.587 2.86 Ferric iron-binding periplasmic protein Q9HTX3...”
• Gene expression in Pseudomonas aeruginosa swarming motility
  Tremblay, BMC genomics 2010
  • “...1.8 PA3655 1 tsf elongation factor Ts 1.7 PA3742 rplS 50S ribosomal protein L19 1.8 PA4255 rpmC 50S ribosomal protein L29 1.7 PA4432 1 rpsI 30S ribosomal protein S9 1.8 PA4567 rpmA 50S ribosomal protein L27 1.5 PA4672 peptidyl-tRNA hydrolase 1.7 PA5049 rpmE 50S ribosomal protein...”
• Toxicogenomic response of Pseudomonas aeruginosa to ortho-phenylphenol
  Nde, BMC genomics 2008
  • “...2.894 0.000276 6.619 0.000276 30S ribosomal protein S18 rps R Translation, post-translational modification, degradation PA4255_rpmC_at PA4255 2.927 0.00331 6.655 0.00331 50S ribosomal protein L29 rpm C Translation, post-translational modification, degradation PA4528_pilD_at PA4528 2.144 0.014 2.65 0.014 type 4 prepilin peptidase PilD pil D Motility & Attachment...”

7unr1 / Q9HWE3 7unr1
53% identity, 93% coverage

• Ligand: rna (7unr1)

SMc01301 PROBABLE 50S RIBOSOMAL PROTEIN L29 from Sinorhizobium meliloti 1021
46% identity, 85% coverage

• Antimicrobial nodule-specific cysteine-rich peptides induce membrane depolarization-associated changes in the transcriptome of Sinorhizobium meliloti
  Tiricz, Applied and environmental microbiology 2013
  • “...0.33 0.46 0.38 0.36 0.41 SMc01299 SMc01300 SMc01301 SMc01302 SMc01303 SMc01304 SMc01305 SMc01306 SMc01307 SMc01308 SMc01309 SMc01310 SMc01313 SMc01314 SMc01318...”
• Absence of functional TolC protein causes increased stress response gene expression in Sinorhizobium meliloti
  Santos, BMC microbiology 2010
  • “...50 S ribosomal protein L14 16.1/13.2 SMc01300 rpsQ probable 30 S ribosomal protein S17 20.8/12.0 SMc01301 rpmC probable 50 S ribosomal protein L29 13.1 SMc01302 rplP probable 50 S ribosomal protein L16 12.4 SMc01303 rpsC probable 30 S ribosomal protein S3 17.5/10.6 SMc01304 rplV probable 50...”

AP064_04705 50S ribosomal protein L29 from Candidatus Liberibacter solanacearum
44% identity, 85% coverage

• Interactions "Candidatus Liberibacter solanacearum"-Bactericera cockerelli: Haplotype Effect on Vector Fitness and Gene Expression Analyses
  Yao, Frontiers in cellular and infection microbiology 2016
  • “...UN 912 58 148 AP064_04425 (64%) CKC_RS05155 50S ribosomal protein L29 689 879 73 238 AP064_04705 (96%) CKC_RS05350 Hypothetical protein 812 938 491 259 AP064_01410 (70%) CKC_RS05630 Hypothetical protein 966 710 65 183 AP064_05100 (91%) CKC_RS05635 Hypothetical protein UN UN 398 470 NONE CKC_RS05640 Hypothetical protein...”

CD16_RS00625 50S ribosomal protein L29 from Candidatus Liberibacter asiaticus
44% identity, 85% coverage

• Establishment of a Cuscuta campestris-mediated enrichment system for genomic and transcriptomic analyses of 'Candidatus Liberibacter asiaticus'
  Li, Microbial biotechnology 2021
  • “...Nucleotide transport and metabolism 4 CD16_RS03415 flgK 1.37 Flagellar hookassociated protein FlgK Cell motility 5 CD16_RS00625 rpmC 1.32 50S ribosomal protein L29 Translation, ribosomal structure and biogenesis 6 CD16_RS02210 CD16_RS02210 1.28 Hypothetical protein Function unknown 7 CD16_RS04785 sufA 1.22 FeS cluster assembly scaffold SufA Function unknown...”

CKC_RS05155 50S ribosomal protein L29 from Candidatus Liberibacter solanacearum CLso-ZC1
44% identity, 85% coverage

• Interactions "Candidatus Liberibacter solanacearum"-Bactericera cockerelli: Haplotype Effect on Vector Fitness and Gene Expression Analyses
  Yao, Frontiers in cellular and infection microbiology 2016
  • “...UN UN 31 73 AP064_04420 (73%) CKC_RS04370 Hypothetical protein UN 912 58 148 AP064_04425 (64%) CKC_RS05155 50S ribosomal protein L29 689 879 73 238 AP064_04705 (96%) CKC_RS05350 Hypothetical protein 812 938 491 259 AP064_01410 (70%) CKC_RS05630 Hypothetical protein 966 710 65 183 AP064_05100 (91%) CKC_RS05635 Hypothetical...”

B7C60_RS03580 50S ribosomal protein L29 from Vibrio fujianensis
58% identity, 95% coverage

• Comparative Genomics and Transcriptomics Analyses Reveal a Unique Environmental Adaptability of Vibrio fujianensis
  Huang, Microorganisms 2020
  • “...rpsH small subunit ribosomal protein S8 Translation B7C60_RS03575 rpsQ small subunit ribosomal protein S17 Translation B7C60_RS03580 rpmC large subunit ribosomal protein L29 Translation B7C60_RS03585 rplP large subunit ribosomal protein L16 Translation B7C60_RS03590 rpsC small subunit ribosomal protein S3 Translation B7C60_RS03595 rplV large subunit ribosomal protein L22...”

RL29_RHOPA / Q6N4U2 Large ribosomal subunit protein uL29; 50S ribosomal protein L29; RRP-L29 from Rhodopseudomonas palustris (strain ATCC BAA-98 / CGA009) (see paper)
RPA3242 50S ribosomal protein L29 from Rhodopseudomonas palustris CGA009
43% identity, 88% coverage

• ATP Is a Major Determinant of Phototrophic Bacterial Longevity in Growth Arrest
  Yin, mBio 2023
  • “...RPA0493, RPA0526, RPA0634, RPA0918, RPA2767, RPA3080, RPA3129, RPA3225, RPA3231, RPA3232, RPA3234, RPA3235, RPA3238, RPA3239, RPA3240, RPA3242, RPA3243, RPA3245, RPA3247-RPA3250, RPA3269, RPA3270, RPA3272, RPA3273, RPA4197, RPA4356; 30S ribosome: RPA0064, RPA0244, RPA0433, RPA1589, RPA2768, RPA2922, RPA3077, RPA3078, RPA3227, RPA3228, RPA3233, RPA3236, RPA3237, RPA3241, RPA3244, RPA3246, RPA3251, RPA3254, RPA3255,...”

RpmC / b3312 50S ribosomal subunit protein L29 from Escherichia coli K-12 substr. MG1655 (see 9 papers)
rpmC / P0A7M6 50S ribosomal subunit protein L29 from Escherichia coli (strain K12) (see 6 papers)
RL29_ECOLI / P0A7M6 Large ribosomal subunit protein uL29; 50S ribosomal protein L29 from Escherichia coli (strain K12) (see 15 papers)
5adyY / P0A7M6 Cryo-em structures of the 50s ribosome subunit bound with hflx (see paper)
P0A7M7 Large ribosomal subunit protein uL29 from Escherichia coli O6:H1 (strain CFT073 / ATCC 700928 / UPEC)
NP_417771 50S ribosomal subunit protein L29 from Escherichia coli str. K-12 substr. MG1655
b3312 50S ribosomal protein L29 from Escherichia coli str. K-12 substr. MG1655
ECs4177 50S ribosomal subunit protein L29 from Escherichia coli O157:H7 str. Sakai
55% identity, 95% coverage

• function: Binds 23S rRNA. It is not essential for growth.
  function: One of the proteins that surrounds the polypeptide exit tunnel on the outside of the subunit. Contacts trigger factor (PubMed:12226666).
  subunit: Part of the 50s ribosomal subunit (PubMed:10094780, PubMed:1092361, PubMed:12809609, PubMed:16272117, PubMed:21499241, PubMed:24844575, PubMed:25310980, PubMed:27906160, PubMed:27906161, PubMed:27934701). Contacts protein L23 (PubMed:2665813), trigger factor (PubMed:12226666) and protein nascent chains (PubMed:12756233). Might also contact SecE and probably does contact SecG when the SecYEG translocation complex is docked with the ribosome (PubMed:16292303).
  disruption phenotype: Cells missing both S17 and L29 grow very slowly and have a rather unstable temperature-sensitive phenotype.
• Ligand: rna (5adyY)
• Protein language models learn evolutionary statistics of interacting sequence motifs.
  Zhang, Proceedings of the National Academy of Sciences of the United States of America 2024
  • “...ESM-2 and a simple linear method, exemplified here for large ribosomal subunit protein RL29 (UniProt: P0A7M7). We can compare the coevolutionary weights obtained from a linear model, calculated using inverse covariance, and the categorical Jacobian calculated from ESM-2. ( C ) Contacts calculated from the categorical...”
• The primary structure of the ribosomal protein L29 from Escherichia coli.
  Bitar, Biochimica et biophysica acta 1975 (PubMed)
  • GeneRIF: N-terminus verified by Edman degradation on complete protein
• CRP and IHF act as host regulators in Royal Jelly's antibacterial activity
  Xia, Scientific reports 2024
  • “...Ribosomal subunit protein L5 rplE 0.25 4.15E08 P60438 Ribosomal subunit protein L3 rplC 0.29 4.88E09 P0A7M6 Ribosomal subunit protein L29 rpmC 0.3 1.35E05 P0A7L0 Ribosomal subunit protein L1 rplA 0.32 6.28E08 P0AG55 Ribosomal subunit protein L6 rplF 0.33 1.98E08 P0A7J7 Ribosomal subunit protein L11 rplK 0.34...”
• Identification of Functional Interactome of Colistin Resistance Protein MCR-1 in Escherichia coli
  Li, Frontiers in microbiology 2020
  • “...50S ribosomal protein L15 14,957 rplO 33 Q0TCE1 50S ribosomal protein L3 22,230 rplC 34 P0A7M6 50S ribosomal protein L29 7,269 rpmC 35 P0A7J3 50S ribosomal protein L10 17,757 rplJ 36 P0AG59 30S ribosomal protein S14 11,630 rpsN 37 P0ABA0 ATP synthase subunit b 17,310 atpF...”
• Capturing Membrane Protein Ribosome Nascent Chain Complexes in a Native-like Environment for Co-translational Studies
  Pellowe, Biochemistry 2020
  • “...RL21, P0AG48; RL22, P61175; RL23, P0ADZ0; RL24, P60624; RL25, P68919; RL27, P0A7M0; RL28, P0A7M2; RL29, P0A7M6; RL30, P0AG51; RL31, P0A7M9; RL32, C4ZS29; RL33, P0A7N9; RL34, P0A7P6; RL35, P0A7Q2; RL36, P0A7Q7. Author Contributions G.A.P., E.R., and P.J.B. designed the research. G.A.P., H.E.F., K.L., T.M.G., and E.R. performed...”
• Top-Down LESA Mass Spectrometry Protein Analysis of Gram-Positive and Gram-Negative Bacteria
  Kocurek, Journal of the American Society for Mass Spectrometry 2017
  • “...room temperature -Met 1019.5584 +5 5092.76 -1.9 SRA P68191 11 1039.4342 +7 7268.99 0.8 L29 P0A7M6 41 Incubation: 24 h, 37 C Storage: 15 days, 4 C 1088.8935 +6 6527.32 -1.1 BhsA a P0AB40 35 -signal peptide 1094.2255 +8 8745.75 -0.6 YnaE P76073 62 1212.1269 +6...”
• Analysis of promoter targets for Escherichia coli transcription elongation factor GreA in vivo and in vitro
  Stepanova, Journal of bacteriology 2007
  • “...rpmC rplP rpsC rplV rpsS rplB rplW rplD rplC rpsJ b3311 b3312 b3313 b3314 b3315 b3316 b3317 b3318 b3319 b3320 b3321 4.2 3.1 3.5 3.2 3.3 3.1 3.1 2.9 3.0 2.3 2.9...”
• YdgG (TqsA) controls biofilm formation in Escherichia coli K-12 through autoinducer 2 transport
  Herzberg, Journal of bacteriology 2006
  • “...b3316 b3319 b3315 b3314 b3637 b0169 b4200 b3186 b4202 b3636 b3983 b3313 b3312 8.6 8 7.5 7.5 7.5 6.1 6.1 6.1 5.3 5.3 5.3 4.9 4.9 4.6 4.3 4 4 50S 50S 50S 30S 30S...”
• Interfering with different steps of protein synthesis explored by transcriptional profiling of Escherichia coli K-12
  Sabina, Journal of bacteriology 2003
  • “...b3104 b1736 b3299 b0011 b1447 b3302 b1451 b2261 b0285 b1600 b0174 b2534 b0154 b3312 b1400 82 77 59 28 27 24 24 20 19 17 16 15 13 12 12 11 9.6 9.4 8.3 8.1 7.9...”
  • “...b4202 b3845 b2447 b3298 b1601 b2272 b4200 b3313 b3057 b0580 b3312 b0833 b3683 b4159 b4201 b3667 b2451 b3065 b3299 b2033 b3301 b1593 b1416 b1189 46 29 27 27 26...”
• Microarray analysis of orthologous genes: conservation of the translational machinery across species at the sequence and expression level
  Jiménez, Genome biology 2003
  • “...L14 Ribosomal protein 12 b3311 Yes** COG0186 J3 30S ribosomal protein S17 Ribosomal protein 12 b3312 Yes** COG0255 J4 50S ribosomal protein L29 Ribosomal protein 12 b3313 Yes** COG0197 J4 50S ribosomal protein L16 Ribosomal protein 12 b3314 Yes** COG0092 J3 30S ribosomal protein S3 Ribosomal...”
• Genome-wide transcriptional profiling of the Escherichia coli responses to superoxide stress and sodium salicylate
  Pomposiello, Journal of bacteriology 2001
  • “...b0113 b4025 b1101 b1658 b3317 b3319 b3305 b3985 b3318 b3312 b3314 b3321 b3316 b0724 b3908 b4062 b0729 b3708 b0850 b2523 b3520 b4217 b1852 acrA ahpC aldA artI...”
  • “...b3313 b3294 b3304 b3186 b3315 b3318 b3309 b3185 b3637 b3312 b3302 b1717 b3299 b3295 b0169 b3314 b3296 b3303 b3306 b3230 b3321 b3297 b3307 b2609 b3311 atpA atpC...”
• Global transcriptional response of Escherichia coli O157:H7 to growth transitions in glucose minimal medium
  Bergholz, BMC microbiology 2007
  • “...rplN -4.46 1 ECs4633 yidB 3.85 2 ECs4176 rpsQ -4.30 1 ECs4672 glmU -2.20 1 ECs4177 rpmC -4.12 1 ECs4674 atpD -2.97 1 ECs4178 rplP -3.60 1 ECs4675 atpG -3.77 1 ECs4179 rpsC -5.07 1 ECs4676 atpA -4.02 1 ECs4180 rplV -4.74 1 ECs4677 atpH -4.50...”

SG4007 50S ribosomal subunit protein L29 from Salmonella enterica subsp. enterica serovar Gallinarum str. 287/91
P66170 Large ribosomal subunit protein uL29 from Salmonella typhimurium (strain LT2 / SGSC1412 / ATCC 700720)
SPC_3501 50S ribosomal protein L29 from Salmonella enterica subsp. enterica serovar Paratyphi C strain RKS4594
SEN3260 50S ribosomal subunit protein L29 from Salmonella enterica subsp. enterica serovar Enteritidis str. P125109
55% identity, 95% coverage

• Deg phenotype of Escherichia coli lon mutants
  Gottesman, Journal of bacteriology 1978
  • “...leu tonA str F' 13 F 8-1 gal+/gal sup' str SG4007 F- sup' gal' lac proC str SG4008 SG4009 SG4010 SG4011 SG12002 SG12008 SG12007 SG12009 SG4030 F- pro' ion-rl...”
  • “...CA7087 (HfrproC Sm' from J. Beckwith) P1 (HR521), to SG4007, select pro' P1 (DT521), to SG4007, select pro' P1 (SA1500), to SG4007, select pro' P1 (SA1384), to...”
• N-dodecanoyl-homoserine lactone influences the levels of thiol and proteins related to oxidation-reduction process in Salmonella
  de, PloS one 2018
  • “...Translation -1.746 2.358 9.704 1.095 0.537 0.297 8.210 1.025 ND ND 50S ribosomal protein L29 P66170 rpmC Translation -1.525 1.640 8.702 1.677 1.191 0.481 -0.900 2.043 0.539 0.280 50S ribosomal protein L30 P0A2A7 rpmD Translation ND ND ND ND ND ND ND ND -9.619 2.532 50S...”
• Antibacterial Components and Modes of the Methanol-Phase Extract from Commelina communis Linn
  Liu, Plants (Basel, Switzerland) 2023
  • “...ribosomal protein L16 SPC_4538 0.34 30S ribosomal protein S6 SPC_3500 0.365 30S ribosomal protein S17 SPC_3501 0.449 50S ribosomal protein L29 SPC_3982 0.484 50S ribosomal protein L1 SPC_0980 4.229 30S ribosomal protein S1 Citrate cycle SPC_2263 0.084 Fumarate hydratase class I aerobic SPC_0731 0.097 Succinate dehydrogenase...”
• Global transcriptomic analysis of ethanol tolerance response in Salmonella Enteritidis
  He, Current research in food science 2022
  • “...S16 SEN3934 rplA 3.52 50S ribosomal protein L1 SEN3275 rpsG 3.56 30S ribosomal protein S7 SEN3260 rpmC 3.70 50S ribosomal protein L29 SEN3253 rplF 3.02 50S ribosomal protein L6 SEN3886 rpmE 3.41 50S ribosomal protein L31 SEN3266 rplW 3.64 50S ribosomal protein L23 SEN3276 rpsL 3.01...”

NP_709100 50S ribosomal subunit protein L29 from Shigella flexneri 2a str. 301
55% identity, 95% coverage

• 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 L24 Cytoplasm No Hits 14 NP_709416 50S ribosomal protein L28 Cytoplasm No Hits 15 NP_709100 50S ribosomal protein L29 Cytoplasm No Hits 16 NP_709090 50S ribosomal protein L30 Cytoplasm No Hits 17 NP_709740 50S ribosomal protein L31 Cytoplasm No Hits 18 NP_707005 50S ribosomal protein...”

Nwi_1372 Ribosomal protein L29 from Nitrobacter winogradskyi Nb-255
38% identity, 90% coverage

• Whole transcriptome analysis highlights nutrient limitation of nitrogen cycle bacteria in simulated microgravity
  Verbeelen, NPJ microgravity 2024
  • “...rpsC 30S ribosomal protein S3 6.20 ND Nwi_1371 rplP 50S ribosomal protein L16 7.22 ND Nwi_1372 rpmC 50S ribosomal protein L29 6.55 3.01 Nwi_1373 rpsQ 30S ribosomal protein S17 5.80 3.45 Nwi_1374 rplN 50S ribosomal protein L14 8.13 3.27 Nwi_1375 rplX 50S ribosomal protein L24 10.18...”

bsl5392 50S ribosomal protein L29 from Bradyrhizobium japonicum USDA 110
45% identity, 85% coverage

• Characterization of a Functional Role of the Bradyrhizobium japonicum Isocitrate Lyase in Desiccation Tolerance
  Jeon, International journal of molecular sciences 2015
  • “...) 50S ribosomal protein L30 1.6 bsl5391 ( rpsQ ) 30S ribosomal protein S17 1.5 bsl5392 ( rpmC ) 50S ribosomal protein L29 1.8 bll5397 ( rplB ) 50S ribosomal protein L2 1.7 bll5415 ( rpl K ) 50S ribosomal Protein L11 2.4 a The differentially-expressed...”
  • “...]. Of the 73 up-regulated genes, 28 overlapped, including five translation-related genes (bll5381, bsl5382, bsl5391, bsl5392, and bll5397), five energy metabolism genes (bll3998, bll4784, bll5655, blr6128, and blr7040), four chaperonins (blr4637, blr4653, blr5625, and blr5626), one transport (bsr4636), one nitrogen fixation (blr2764), one regulatory gene (blr2475),...”

6spbY / W6V2V8 Pseudomonas aeruginosa 50s ribosome from a clinical isolate with a mutation in ul6 (see paper)
63% identity, 67% coverage

• Ligand: rna (6spbY)

SG2270 50S ribosomal protein L29 from Sodalis glossinidius str. 'morsitans'
53% identity, 95% coverage

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

bglu_1g02660 50S ribosomal protein L29 from Burkholderia glumae BGR1
55% identity, 73% coverage

• RNAseq-based Transcriptome Analysis of Burkholderia glumae Quorum Sensing
  Kim, The plant pathology journal 2013
  • “...0.9 1.6 1.5 bglu_1g02640 rpsC 1.4 1 1.6 1.3 bglu_1g02650 rplP 1.5 1.1 1.5 1.3 bglu_1g02660 rpm 1.4 1 1.7 1.4 bglu_1g02670 rpsQ 1.3 0.9 1.4 1.3 bglu_1g0268 rplN 1.3 0.9 1.7 1.9 bglu_1g02690 rplX 1.1 0.8 1.5 1.7 bglu_1g02700 rplE 1.2 0.8 1.4 1.7 bglu_1g02710...”

YPO0218 50S ribosomal protein L29 from Yersinia pestis CO92
52% identity, 95% coverage

• Comparative Global Gene Expression Profiles of Wild-Type Yersinia pestis CO92 and Its Braun Lipoprotein Mutant at Flea and Human Body Temperatures
  Galindo, Comparative and functional genomics 2010
  • “...protein L15 rplO Protein synthesis 11.4 YPO0225 50S ribosomal protein L18 rplR Protein synthesis 8.7 YPO0218 50S ribosomal protein L29 rpmC Protein synthesis 11.6 y0299 50S ribosomal subunit protein L31 rpmE Protein synthesis 15.1 Transport YPO2672 putative urea transporter Transport and binding proteins 33.3 YPO3156 ATP-dependent...”

CD0080A 50S ribosomal protein L29 from Clostridium difficile 630
38% identity, 91% coverage

• Genome Location Dictates the Transcriptional Response to PolC Inhibition in Clostridium difficile
  van, Antimicrobial agents and chemotherapy 2019
  • “...CD1794 CD2355 CD630DERM_17940 CD630DERM_23550 CD3175 CD0080A CD0072 CD3031 CD3663 CD0093 CD3206 CD3174 CD630DERM_32060 CD630DERM_31740 CD630DERM_31750...”
• Transcriptional profiling of Clostridium difficile and Caco-2 cells during infection
  Janvilisri, The Journal of infectious diseases 2010
  • “...up-regulation of genes encoding (i) ribosomal proteins such as rplW ( CD0075 ), rpmC ( CD0080A ), rpsZ ( CD0084A ), and CD0093 ; (ii) ribosomal protein methyltransferase prmA ( CD2450 ); (iii) DNA repair proteins such as recJ ( CD2746 ) and CD3398 , as...”

FTN_0247 50S ribosomal protein L29 from Francisella tularensis subsp. novicida U112
40% identity, 86% coverage

• Importance of host cell arginine uptake in Francisella phagosomal escape and ribosomal protein amounts
  Ramond, Molecular & cellular proteomics : MCP 2015
  • “...FTN_0916 FTN_0676 FTN_0675 FTN_0608 FTN_0265 FTN_0257 FTN_0256 FTN_0247 FTN_0243 FTN_0242 FTN_0235 FTN_0159 rpsP rpmE rpsK rpsM rplN rplP rpsC rpsG rplA...”

FTL_0244 50S ribosomal protein L29 from Francisella tularensis subsp. holarctica
FTH_0239 ribosomal protein L29 from Francisella tularensis subsp. holarctica OSU18
40% identity, 86% coverage

• Use of a capture-based pathogen transcript enrichment strategy for RNA-Seq analysis of the Francisella tularensis LVS transcriptome during infection of murine macrophages
  Bent, PloS one 2013
  • “...shock -5.03 <0.001 FTL_1796 ATP synthase -subunit -9.71 <0.001 FTL_0965 hslV /heat shock -7.19 0.005 FTL_0244 L29 ribosomal protein -11.24 <0.001 FTL_1128 Unknown * -10.80 <0.001 FTL_0238 rplW /ribosomal protein -11.49 <0.001 * Genes encoding products with unknown function 10.1371/journal.pone.0077834.g002 Figure 2 Comparison of the genes...”
• Use of magnetic hydrazide-modified polymer microspheres for enrichment of Francisella tularensis glycoproteins
  Horák, Soft matter 2012
  • “...cyt FTH_0237 Ribosomal protein S3 24.88/10.10 cyt cyt FTH_0238 Ribosomal protein L16 15.71/11.43 cyt cyt FTH_0239 Ribosomal protein L29 7.80/10.34 cyt cyt FTH_0241 Ribosomal protein L14 13.23/10.51 cyt cyt FTH_0242 50S ribosomal protein L24 11.48/9.73 cyt cyt FTH_0243 Ribosomal protein L5 20.00/9.75 cyt cyt FTH_0246 Ribosomal...”
  • “...cyt FTH_0237 Ribosomal protein S3 24.88/10.10 cyt cyt FTH_0238 Ribosomal protein L16 15.71/11.43 cyt cyt FTH_0239 Ribosomal protein L29 7.80/10.34 cyt cyt FTH_0241 Ribosomal protein L14 13.23/10.51 cyt cyt FTH_0242 50S ribosomal protein L24 11.48/9.73 cyt cyt FTH_0243 Ribosomal protein L5 20.00/9.75 cyt cyt FTH_0244 30S...”

CA_C3125 50S ribosomal protein L29 from Clostridium acetobutylicum ATCC 824
CAC3125 Ribosomal protein L29 from Clostridium acetobutylicum ATCC 824
39% identity, 85% coverage

• Clostridium acetobutylicum grows vegetatively in a biofilm rich in heteropolysaccharides and cytoplasmic proteins
  Liu, Biotechnology for biofuels 2018
  • “...shock protein 11 CA_C1834 448 9203 19 4 5.9 Host factor I protein Hfq 12 CA_C3125 299 7908 7 3 5.4 Ribosomal protein L29 13 CA_C2712 571 28,400 28 10 4.9 Crotonase 14 CA_C1807 182 10,251 7 5 4.8 Ribosomal Protein S15 15 CA_C3211 1113 10,341...”
• Complex and extensive post-transcriptional regulation revealed by integrative proteomic and transcriptomic analysis of metabolite stress response in Clostridium acetobutylicum
  Venkataramanan, Biotechnology for biofuels 2015
  • “...to note that a few ribosomal proteins were upregulated, including those coded by CAC1787, CAC3097, CAC3125, CAC3132, and CAC3147 thus suggesting that the cells may employ an alternate set of protein for protein synthesis under stress. Along the same lines, under butyrate stress, there were a...”

A1JS26 Large ribosomal subunit protein uL29 from Yersinia enterocolitica serotype O:8 / biotype 1B (strain NCTC 13174 / 8081)
52% identity, 95% coverage

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

9c4gx / A0A2B7JB12 Cutibacterium acnes 50s ribosomal subunit with clindamycin bound (see paper)
40% identity, 83% coverage

• Ligand: rna (9c4gx)

A1S_3073 50S ribosomal protein L29 from Acinetobacter baumannii ATCC 17978
AbA118F_2933 50S ribosomal protein L29 from Acinetobacter baumannii
42% identity, 92% coverage

• Insights Into Mechanisms of Biofilm Formation in Acinetobacter baumannii and Implications for Uropathogenesis
  Colquhoun, Frontiers in cellular and infection microbiology 2020
  • “...3.78, 2.26 AB5075_UW, ATCC 17978 Rumbo-Feal et al., 2013 ; Penesyan et al., 2019 rpmC A1S_3073 50S ribosomal protein L29 4.45, 2.01 AB5075_UW, ATCC 17978 Rumbo-Feal et al., 2013 ; Penesyan et al., 2019 rplB A1S_3077 50S ribosomal protein L2 5.63, 1.75 AB5075_UW, ATCC 17978 Rumbo-Feal...”
• Whole transcriptome analysis of Acinetobacter baumannii assessed by RNA-sequencing reveals different mRNA expression profiles in biofilm compared to planktonic cells
  Rumbo-Feal, PloS one 2013
  • “...2.27 A1S_3069 50S ribosomal protein L5 2.13 1.66 A1S_3070 50S ribosomal protein L24 2.26 2.05 A1S_3073 50S ribosomal protein L29 2.01 3.00 A1S_3074 50S ribosomal protein L16 2.05 3.56 A1S_3075 30S ribosomal protein S3 1.73 3.06 A1S_3077 50S ribosomal protein L2 1.75 1.77 A1S_3079 50S ribosomal...”
• Cerebrospinal fluid (CSF) augments metabolism and virulence expression factors in Acinetobacter baumannii
  Martinez, Scientific reports 2021
  • “...carboxylase AbA118F_0483 2.14 1.2 E-107 ATP synthase delta chain AbA118F_1447 2.12 6.7 E-08 hypothetical protein AbA118F_2933 rpmC 2.12 4.5 E-85 LSU ribosomal protein L29p (L35e)- rpmC AbA118F_1014 2.10 1.5 E-78 fimbrial adhesin precursor AbA118F_2505 2.09 1.4 E-58 Biotin carboxyl carrier protein of acetyl-CoA carboxylase AbA118F_3136 2.09...”

RL29_BACSU / P12873 Large ribosomal subunit protein uL29; 50S ribosomal protein L29 from Bacillus subtilis (strain 168) (see paper)
8buuY / P12873 8buuY (see paper)
BSU01240 50S ribosomal protein L29 from Bacillus subtilis subsp. subtilis str. 168
39% identity, 86% coverage

• subunit: Part of the 50S ribosomal subunit.
• Ligand: rna (8buuY)
• The Blueprint of a Minimal Cell: MiniBacillus
  Reuß, Microbiology and molecular biology reviews : MMBR 2016
  • “...BSU27960 BSU01210 BSU01180 BSU01270 BSU27940 BSU15820 BSU01240 BSU01340 BSU37070 BSU15080 BSU24900 BSU00990 BSU41060 BSU28860 BSU01400 BSU16490 BSU01220...”

FN1637 LSU ribosomal protein L29P from Fusobacterium nucleatum subsp. nucleatum ATCC 25586
38% identity, 95% coverage

• Proteomics of Fusobacterium nucleatum within a model developing oral microbial community
  Hendrickson, MicrobiologyOpen 2014
  • “...FN1437, FN1557, FN1558, FN1620, FN1623, FN1625, FN1626, FN1627, FN1628, FN1629, FN1630, FN1631, FN1632, FN1634, FN1635, FN1637, FN1638, FN1639, FN1640, FN1641, FN1642, FN1643, FN1644, FN1645, FN1646, FN1656, FN1657, FN1781, FN1828, FN1879, FN1979, FN2037, FN2038, FN2039, FN2040. 3 Covers FN0040, FN0054, FN0067, FN0069, FN0070, FN0110, FN0298, FN0299, FN0405,...”

D4G3L1 Large ribosomal subunit protein uL29 from Bacillus subtilis subsp. natto (strain BEST195)
39% identity, 81% coverage

• Proteomic Response of Bacillus subtilis Spores under High Pressure Combined with Moderate Temperature and Random Peptide Mixture LK Treatment
  Pang, Foods (Basel, Switzerland) 2022
  • “...homolog (P38494), 30S ribosomal protein (S2P21464), 50S ribosomal protein L13 (M4KMS5), 50S ribosomal protein L29 (D4G3L1), 30S ribosomal protein S4 (A0A4R6HVR7), and 30S ribosomal protein S14 (A0A5D4N259). Among the upregulated proteins, in the TCA cycle pathway, the 2-oxoglutarate dehydrogenase E1 component (P23129), the E1 component of...”
  • “...S2 P21464 0.03 0.13 50S ribosomal protein L13 M4KMS5 0.03 0.13 50S ribosomal protein L29 D4G3L1 0.03 0.13 30S ribosomal protein S4 A0A4R6HVR7 0.03 0.13 30S ribosomal protein S14 A0A5D4N259 0.03 0.13 Oxidative phosphorylation Quinol oxidase subunit 1 P34956 0.02 0.15 ATP synthase subunit c P37815...”

MHO_2900 50S ribosomal protein L29 from Mycoplasma hominis
35% identity, 91% coverage

• Genome-wide Analysis of Mycoplasma hominis for the Identification of Putative Therapeutic Targets
  Parvege, Drug target insights 2014
  • “...Novel 53 MHO_2870 50S ribosomal protein L24 Cytoplasm 0 No (76) 50 No Novel 54 MHO_2900 50S ribosomal protein L29 Cytoplasm 0 No (79) 50 No Novel 55 MHO_3020 50S ribosomal protein L31 Cytoplasm 0 No (78) 50 No Novel 56 MHO_3920 50S ribosomal protein L9...”

SAUSA300_2196 50S ribosomal protein L29 from Staphylococcus aureus subsp. aureus USA300_FPR3757
38% identity, 77% coverage

• Heparin Mimics Extracellular DNA in Binding to Cell Surface-Localized Proteins and Promoting Staphylococcus aureus Biofilm Formation
  Mishra, mSphere 2017
  • “...30 None SAUSA300_1052 Fibrinogen-binding protein 3 3 21 FKRTRTTHRKAQRA SAUSA300_0964 Chitinase 2 2 18 None SAUSA300_2196 50S ribosomal protein L29 3 2 32 None SAUSA300_0801 Enterotoxin, Seq 3 3 18 NKTKKGIKLRKY SAUSA300_0883 Putative surface protein 4 5 42 None SAUSA300_2195 30S ribosomal protein S17 2 2...”

SACOL2231 ribosomal protein L29 from Staphylococcus aureus subsp. aureus COL
Q6GEJ1 Large ribosomal subunit protein uL29 from Staphylococcus aureus (strain MRSA252)
SA2039 50S ribosomal protein L29 from Staphylococcus aureus subsp. aureus N315
SAOUHSC_02504 ribosomal protein L29 from Staphylococcus aureus subsp. aureus NCTC 8325
SERP1823 ribosomal protein L29 from Staphylococcus epidermidis RP62A
EKM74_RS05590, USA300HOU_RS12135 50S ribosomal protein L29 from Staphylococcus aureus
38% identity, 81% coverage

• The Staphylococcus aureus LytSR two-component regulatory system affects biofilm formation
  Sharma-Kuinkel, Journal of bacteriology 2009
  • “...SACOL1725 SACOL1702 SACOL2234 SACOL2237 SACOL2228 SACOL2231 SACOL2221 SACOL1726 SACOL1274 SACOL2233 SACOL2222 SACOL0592 SACOL2240 SACOL2214 SACOL0591 SACOL2226...”
• Structural and Functional Dynamics of Staphylococcus aureus Biofilms and Biofilm Matrix Proteins on Different Clinical Materials
  Hiltunen, Microorganisms 2019
  • “...Q99WA2 50S ribosomal protein L27 Q931Q3 50S ribosomal protein L28 Q6GHL1 50S ribosomal protein L29 Q6GEJ1 50S ribosomal protein L3 Q6GEI3 50S ribosomal protein L30 Q6GEK1 50S ribosomal protein L31 Q6GEV5 50S ribosomal protein L35 Q6GG26 50S ribosomal protein L4 Q6GEI4 50S ribosomal protein L5 Q99S33...”
• Molecular Evolutionary Pathways toward Two Successful Community-Associated but Multidrug-Resistant ST59 Methicillin-Resistant Staphylococcus aureus Lineages in Taiwan: Dynamic Modes of Mobile Genetic Element Salvages
  Hung, PloS one 2016 (no snippet)
• Analysis of the matrix-assisted laser desorption ionization-time of flight mass spectrum of Staphylococcus aureus identifies mutations that allow differentiation of the main clonal lineages
  Josten, Journal of clinical microbiology 2013
  • “...cloning of antisense products rpmJ (SAS078) SAR1012 rpmC (SA2039) rpsT (SA1414) hup (SA1305) Primers used for PCR and sequencing of genes hld (SAOUHSC_02260)...”
  • “...rpmF (SAS033) rpmD (SA2030) SA1452 graC (SAS044) SA2039 rpsP (SA1081) Primer sequence SAS078for SAS078rev SAR1012for SAR1012rev SA0772for SA0772rev SA2039for...”
• Transcriptional profiles of the response of methicillin-resistant Staphylococcus aureus to pentacyclic triterpenoids
  Chung, PloS one 2013
  • “...rpmA 50S ribosomal protein L27 6.3 Translation SA1067 rpmB 50S ribosomal protein L28 6.3 Translation SA2039 rpmC 50S ribosomal protein L29 9.4 Translation SA2047 rplC 50S ribosomal protein L3 4.9 Translation SA2030 rpmD 50S ribosomal protein L30 6.2 Translation SA1922 rpmE 50S ribosomal protein L31 type...”
• High throughput multiple locus variable number of tandem repeat analysis (MLVA) of Staphylococcus aureus from human, animal and food sources
  Sobral, PloS one 2012
  • “...Sa1194, Sa1729, Sa1866. PCR reaction 2 amplifies the six VNTR loci Sa0266, Sa0704, Sa1132, Sa1291, Sa2039, Sa2511 ( Tables 2 and 3 ). VNTRs Sa0122 and Sa0266 are located in the genes spa and coa respectively. VNTRs Sa0311, Sa1729 and Sa1866 are members of the family...”
  • “...Sa1729 56 X X X Sa1756 131 SIRU15 c X Sa1866 129 X X X Sa2039 56 X X X Sa2511 61 VNTR61_01 d X X a the VNTR locus name reflects genome localisation (in kb) in strain Mu50 refseq NC_002758. b alternative names given in...”
• Longitudinal survey of Staphylococcus aureus in cystic fibrosis patients using a multiple-locus variable-number of tandem-repeats analysis method
  Vu-Thien, BMC microbiology 2010
  • “...56 5 L TACTTAAAAATARGAATACATAATTAG STAR R CAACAATAAATTACTTATTTGAAGTT Sa1866 159 3 L CTGTTTTGCAGCGTTTGCTA SAV1738 R GCAACTTGAAGAAACGGTTG Sa2039 56 3 L TTCGTTCTACCCCAACTTGC STAR R GAGCCTGGGTCATAAATTCAA Sa1756 e 131 1 L AATTATAGCATATTAGAGCCCCTTA 50S ribosomal protein L27 Alias SIRU15 R ACGTAAAGGTCGCGACAAAA a The chromosomal position on the Mu50 genome, in...”
  • “...spa ), Sa0266 (alias coa ), Sa0311, Sa0704, Sa1132, Sa1194, Sa1291 (alias SIRU13), Sa1729, Sa1866, Sa2039, Sa0906, Sa1213, Sa1425 and Sa1756 (alias SIRU15). The genotype of the Mu50 strain deduced from its genomic sequence is 10 6 3 4 6 7 4 5 3 3 3...”
• Characterizing the effects of inorganic acid and alkaline shock on the Staphylococcus aureus transcriptome and messenger RNA turnover
  Anderson, FEMS immunology and medical microbiology 2010
  • “...high affinity proline permease sa_c4189s3541_a_at 4.9 2.5 2.5 SA2038 O-sialoglycoprotein endopeptidase sa_c4197s3549_at 7.3 2.5 2.5 SA2039 putative ribosomal-protein-alanine acetyltransferase sa_c9831s8573_a_at 4.2 2.5 2.5 SA2107 phosphotyrosine phosphatase sa_c4460s3803_a_at * 3.6 2.5 2.5 SA2109 modification methylase sa_c5126s4423_a_at * 4.2 2.5 2.5 SA2309 amino acid permease sa_c5389s4662_a_at 3.6 2.5...”
• Improved multiple-locus variable-number tandem-repeat assay for Staphylococcus aureus genotyping, providing a highly informative technique together with strong phylogenetic value
  Pourcel, Journal of clinical microbiology 2009
  • “...Sa0704, Sa1132, Sa1194, Sa1291 (SIRU13), Sa1729, Sa1866, and Sa2039 (panel 1) and Sa0906, Sa1213, Sa1425, and Sa1756 (SIRU15) (panel 2) (Table 1). The genotype...”
  • “...Sa1194 67 7 524 64 4 369 Sa1729 56 5 499 Sa1866 159 3 607 Sa2039 56 3 282 Panel 2 Sa0906 56 3 864 Sa1213 56 5 868 Sa1425 58 4 630 131 2 365 15 5 257 Panel 1...”
• Microarray analysis of toxicogenomic effects of ortho-phenylphenol in Staphylococcus aureus
  Jang, BMC genomics 2008
  • “...ribosomal protein S17; ribosomal protein S17 (BS16) rps Q Translation, ribosomal structure and biogenesis sa_c4860s4166_at SA2039 0.00204 2.5 50S ribosomal protein L29; ribosomal protein L29 rpm C Translation, ribosomal structure and biogenesis sa_c4864s4170_at SA2040 0.000749 2.7 50S ribosomal protein L16; ribosomal protein L16 rpl P Translation,...”
• More
• Antibacterial Components and Modes of the Methanol-Phase Extract from Commelina communis Linn
  Liu, Plants (Basel, Switzerland) 2023
  • “...0.326 Ribosomal protein L30 SAOUHSC_02494 0.353 Ribosomal protein S5 SAOUHSC_02499 0.358 Ribosomal protein S14p/S29e putative SAOUHSC_02504 0.360 Ribosomal protein L29 SAOUHSC_02492 0.369 Ribosomal protein L15 SAOUHSC_02498 0.383 Ribosomal protein S8 putative SAOUHSC_02487 0.383 Conserved hypothetical protein SAOUHSC_02495 0.384 Ribosomal protein L18 SAOUHSC_02496 0.389 Ribosomal protein L6...”
• Copper stress in Staphylococcus aureus leads to adaptive changes in central carbon metabolism
  Tarrant, Metallomics : integrated biometal science 2019
  • “...d -Alanine-poly(phosphoribitol) ligase subunit 1 dltA SAOUHSC_00869 gi|122539917 1.4 <0.00010 50S ribosomal protein L29 rpmC SAOUHSC_02504 gi|122538860 1.4 0.00017 2,3-Bisphosphoglycerate-dependent phosphoglycerate mutase gpmA SAUOHSC_02703 gi|122538743 1.1 <0.00010 Alkyl hydroperoxide reductase subunit C ahpC SAOUHSC_00365 gi|60391219 1.1 <0.00010 Catalase katA SAOUHSC_01327 gi|126215678 <1.1 <0.00010 Proteins with decreased...”
• Suppression of Staphylococcus aureus biofilm formation and virulence by a benzimidazole derivative, UM-C162
  Kong, Scientific reports 2018
  • “...induced and suppressed by UM-C162. Function No. of genes Genes P value Up-regulated Translation 30 SAOUHSC_02504, SAOUHSC_01666, rpsC , rpsD , rpsE , rpsH , rpsJ , rpsQ , rpsS , rpsT , rplB , rplC , rplD , rplE , rplF , rplJ , rplN...”
• Concentration-Dependent Global Quantitative Proteome Response of Staphylococcus epidermidis RP62A Biofilms to Subinhibitory Tigecycline
  Sung, Cells 2022
  • “...L24 2.71 2.98 2.39 SERP1821 rplN fig|176279.9.peg.1778 J 50S ribosomal protein L14 1.70 1000.00 33.34 SERP1823 rpmC fig|176279.9.peg.1780 J 50S ribosomal protein L29 4.32 6.88 9.17 SERP1824 rplP fig|176279.9.peg.1781 J 50S ribosomal protein L16 1000.00 1000.00 72.77 SERP1825 rpsC fig|176279.9.peg.1782 J 30S ribosomal protein S3 0.00...”
  • “...L14 1.70 1000.00 33.34 SERP0187 rpsG fig|176279.9.peg.178 J 30S ribosomal protein S7 11.20 11.48 13.52 SERP1823 rpmC fig|176279.9.peg.1780 J 50S ribosomal protein L29 4.32 6.88 9.17 SERP1824 rplP fig|176279.9.peg.1781 J 50S ribosomal protein L16 1000.00 1000.00 72.77 SERP1825 rpsC fig|176279.9.peg.1782 J 30S ribosomal protein S3 0.00...”
• Impact of the Staphylococcus epidermidis LytSR two-component regulatory system on murein hydrolase activity, pyruvate utilization and global transcriptional profile
  Zhu, BMC microbiology 2010
  • “...rplX 50 S ribosomal protein L24 0.356 SERP1822 rpsQ 30 S ribosomal protein S17 0.344 SERP1823 rpmC 50 S ribosomal protein L29 0.332 SERP1824 rplP 50 S ribosomal protein L16 0.438 SERP1825 rpsC 30 S ribosomal protein S3 0.345 SERP1826 rplV 50 S ribosomal protein L22...”
• Transcriptomic Analysis Revealed Antimicrobial Mechanisms of Lactobacillus rhamnosus SCB0119 against Escherichia coli and Staphylococcus aureus
  Peng, International journal of molecular sciences 2022
  • “...ribosomal protein L14 EKM74_RS05585 140.46 16.11 4981.9 113.47 5.148408 rpsQ ; 30S ribosomal protein S17 EKM74_RS05590 154.79 34.38 4723.29 418.72 4.931395 rpmC ; 50S ribosomal protein L29 EKM74_RS05595 194.99 8.39 3442.61 618.09 4.142009 rplP ; 50S ribosomal protein L16 EKM74_RS05600 333.68 100.38 6017.46 493.68 4.172617 rpsC...”
• Absence of Protoheme IX Farnesyltransferase CtaB Causes Virulence Attenuation but Enhances Pigment Production and Persister Survival in MRSA
  Xu, Frontiers in microbiology 2016
  • “...USA300HOU_RS04630 dltC 2.11 7.32E-03 D-alaninepoly(phosphoribitol) ligase USA300HOU_RS08560 2.07 1.27E-02 Acetyl-CoA carboxylase biotin carboxyl carrier subunit USA300HOU_RS12135 rpmC 2.04 3.26E-03 Ribosomal protein L29 USA300HOU_RS11075 ilvC 2.03 1.12E-02 Ketol-acid reductoisomerase USA300HOU_RS00655 2.03 3.65E-02 Hypothetical membrane protein USA300HOU_RS01875 2.01 4.74E-02 Hypothetical protein USA300HOU_RS04875 fabH1 1.95 4.11E-03 3-oxoacyl-[acyl-carrier-protein] synthase USA300HOU_RS02840...”

6v39X / B7IA31 6v39X (see paper)
41% identity, 94% coverage

• Ligand: rna (6v39X)

lmo2624 ribosomal protein L29 from Listeria monocytogenes EGD-e
Q71WF4 Large ribosomal subunit protein uL29 from Listeria monocytogenes serotype 4b (strain F2365)
40% identity, 90% coverage

• SecA2 Associates with Translating Ribosomes and Contributes to the Secretion of Potent IFN-β Inducing RNAs
  Teubner, International journal of molecular sciences 2022
  • “...Lipid transport and metabolism 1.70 2.16 lmo1330 rpsO 30S ribosomal protein S15 Translation 2.32 2.15 lmo2624 rpmC 50S ribosomal protein L29 Translation 1.60 2.09 lmo2016 cspB Cold shock-like protein CspLB Transcription 1.51 1.98 lmo1473 * dnaK Chaperone protein DnaK Posttranslational modification. protein turnover. chaperones 1.72 1.96...”
• Whole genome genetic variation and linkage disequilibrium in a diverse collection of Listeria monocytogenes isolates
  Louha, PloS one 2021
  • “...w.r.t. BIGSdb- Lm Function lmo0046 rpsR 19 0.85 50514..50753 core small subunit ribosomal protein S18 lmo2624 rpmC 185 8.289 2701254..2701445 core large subunit ribosomal protein L29 lmo2856 rpmH 215 9.63 2943569..2943703 accessory large subunit ribosomal protein L34 lmo1364 cspL 239 10.71 1387014..1387214 accessory Cold shock protein...”
  • “...in the genome. A large number (~41%) of these hot spot genes ( lmo0046 , lmo2624 , lmo2856 , lmo1469 , lmo2616 , lmo1816 , lmo0248 , lmo1335 , lmo2047 , lmo2628 , lmo2614 ), encode ribosomal proteins and their related subunits. According to the complexity...”
• Transcriptomic and Phenotypic Analyses of the Sigma B-Dependent Characteristics and the Synergism between Sigma B and Sigma L in Listeria monocytogenes EGD-e
  Mattila, Microorganisms 2020
  • “...L5 1.9 1.7 lmo2621 ribosomal protein L24 1.7 1.5 lmo2622 ribosomal protein L14 1.5 1.6 lmo2624 ribosomal protein L29 1.9 1.5 lmo2625 ribosomal protein L16 1.8 1.5 lmo2626 ribosomal protein S3 1.6 1.5 Purines, pyrimidines, nucleosides, and nucleotides lmo2611 adenylate kinase 1.5 1.9 Regulatory functions lmo1956...”
• 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
  • “...0.952 Non-allergen 144 Q721N6 0.586 Non-allergen 145 Q71ZK1 1.532 Non-allergen 146 Q71ZD0 1.746 Non-allergen 147 Q71WF4 0.935 Non-allergen 148 Q71YL9 2.126 Non-allergen 149 Q71WG9 1.537 Non-allergen 150 Q71YK0 2.221 Non-allergen 151 Q71WI2 2.143 Non-allergen 152 Q71VQ6 1.957 Non-allergen 153 Q724G8 1.5 Non-allergen 154 Q722D6 1.506 Non-allergen...”
  • “...18 1.5447 Antigen Q71ZK1 DRB1_1301 KKSEAARKR 46.5 1.9356 Antigen Q71ZD0 DRB1_1301 MLKFDIQHF 45 1.2032 Antigen Q71WF4 DRB1_0101 LFNLRFQLA 1029 2.5288 Antigen Q71YL9 DRB1_1301 MAVKIRLKR 4.3 1.4155 Antigen DRB1_1301 AVKIRLKRI 55.1 1.4342 Antigen Q71YK0 DRB1_1301 RKSRSGNKR 40.5 2.7338 Antigen Q71WI2 DRB1_1301 LLTRDPRMK 16.6 1.3863 Antigen DRB1_1301 KSSVARVRL...”

P58085 Large ribosomal subunit protein uL29 from Aeropyrum pernix (strain ATCC 700893 / DSM 11879 / JCM 9820 / NBRC 100138 / K1)
42% identity, 80% coverage

• Re-annotation of genome microbial coding-sequences: finding new genes and inaccurately annotated genes
  Bocs, BMC bioinformatics 2002
  • “...Entry Accession Description Seq Length (aa) RL21_AERPE P58077 50S RIBOSOMAL PROTEIN L21 E 107 RL29_AERPE P58085 50S RIBOSOMAL PROTEIN L29P 66 RL34_AERPE P58026 50S RIBOSOMAL PROTEIN L34E 95 GYRB_ARCFU 029720 DNA GYRASE SUBUNIT B (EC 5.99.1.3) 632 EX7S_CHLTR P58001 PROBABLE EXODEOXYRIBONUCLEASE VII SMALL SUBUNIT (EC 3.1.11.6)...”

NCgl0495 50S ribosomal protein L29 from Corynebacterium glutamicum ATCC 13032
cg0603 50S ribosomal protein L29 from Corynebacterium glutamicum ATCC 13032
50% identity, 61% coverage

• Transcriptome analysis of Corynebacterium glutamicum in the process of recombinant protein expression in bioreactors
  Sun, PloS one 2017
  • “...that were hypothetical proteins. Eleven genes encoded ribosomal proteins (NCgl1304, NCgl0538, NCgl1901, NCgl2261, NCgl0518, NCgl0515, NCgl0495, NCgl0487, NCgl0833, NCgl1325, NCgl0488); however, most of them were down-regulated under C . glutamicum EGFP, indicating that the translation process was suppressed with EGFP expression. There were two genes (NCgl0303,...”
• Functional genomics of pH homeostasis in Corynebacterium glutamicum revealed novel links between pH response, oxidative stress, iron homeostasis and methionine synthesis
  Follmann, BMC genomics 2009
  • “...protein L16/L10E 0 -1.02 -0.27 3.1 3.3 3.1 4.5 4.8 5.0 3.0 3.4 3.5 24 cg0603 g rpmC 50S ribosomal protein L29 0 -1.01 -0.20 - -0.8 - - - - - - - 25 cg0604 g rpsQ 30S ribosomal protein S17 0 -1.18 -0.21 3.3...”

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.