PaperBLAST
PaperBLAST Hits for OH686_13630 (78 a.a., MSRVCQVTGK...)
Show query sequence
>OH686_13630
MSRVCQVTGKGPVTGNNVSHANNKTRRRFLPNLQHHRFWVESEKRFVRLRVSAKGMRIID
KRGIDVVLSELRARGEKV
Running BLASTp...
Found 69 similar proteins in the literature:
PA5316 50S ribosomal protein L28 from Pseudomonas aeruginosa PAO1
PA14_70190 50S ribosomal protein L28 from Pseudomonas aeruginosa UCBPP-PA14
92% identity, 99% coverage
- Virtual Screening and Meta-Analysis Approach Identifies Factors for Inversion Stimulation (Fis) and Other Genes Responsible for Biofilm Production in <i>Pseudomonas aeruginosa</i>: A Corneal Pathogen
Emeka, Current issues in molecular biology 2024 - “...of biofilms, supporting the studys conclusions. The top-ranked up-regulated genes are 50S ribosomal protein L28 (PA5316; rpmB), rod shape-determining protein MreC (PA4480; mreC), and translation initiation factor IF-2 (PA4744; infB) that were previously implicated in resistance to tobramycin and biofilm formation in P. aeruginosa [ 47...”
- “...up-regulated genes in biofilm. Locus Tag Gene Symbol Gene Name Combined Effect Size Padj Value PA5316 rpmB 50S ribosomal protein L28 3.01 1.57 10 8 PA4257 rpsC 30S ribosomal protein S3 2.63 4.86 10 10 PA4239 rpsD 30S ribosomal protein S4 2.47 1.58 10 8 PA3743...”
- Distinct transcriptome and traits of freshly dispersed <i>Pseudomonas aeruginosa</i> cells
Kalia, mSphere 2024 - “...0.483919 Upregulated 1.052386 PA4430 Cytochrome B Upregulated 1.244303 Upregulated 0.843705 PA4658 Upregulated 0.939783 Upregulated 1.015749 PA5316 Upregulated 1.352634 Upregulated 1.400194 PA5367 pstA-phosphate ABC transporter permease Upregulated 2.119658 Upregulated 1.54155 PA5368 pstC-phosphate ABC transporter permease Upregulated 1.776169 Upregulated 1.306284 PA5369 pstS-(PA5369) phosphate ABC transporter substrate-binding protein Upregulated...”
- Multidrug Adaptive Resistance of Pseudomonas aeruginosa Swarming Cells
Coleman, Antimicrobial agents and chemotherapy 2020 (secret) - Molecular mechanism for sphingosine-induced Pseudomonas ceramidase expression through the transcriptional regulator SphR
Okino, Scientific reports 2016 - “...protein 1.602 0.0019591 PA3446 conserved hypothetical protein 1.597 0.0080397 PA0277 conserved hypothetical protein 1.594 0.0476063 PA5316 rpmB 50S ribosomal protein L28 1.594 0.0217275 PA0662 argC N-acetyl-gamma-glutamyl-phosphate reductase 1.591 0.0290015 PA2062 probable pyridoxal-phosphate dependent enzyme 1.587 0.0163330 PA5192 pckA phosphoenolpyruvate carboxykinase 1.572 0.0085155 PA3745 rpsP 30S ribosomal...”
- Analysis of Pseudomonas aeruginosa cell envelope proteome by capture of surface-exposed proteins on activated magnetic nanoparticles
Vecchietti, PloS one 2012 - “...antitermination protein NusG 2 C,3 + rplJ PA4272 50S rP L10 2 C,3 + rpmB PA5316 50S rP L28 2 C,3 + rpsC PA4257 30S rP S3 2 C,3 + rpsB PA3656 30S rP S2 2 C,3,P,1 + rpsP PA3745 30S rP S16 2 C,3 +...”
- Transcriptional and proteomic responses of Pseudomonas aeruginosa PAO1 to spaceflight conditions involve Hfq regulation and reveal a role for oxygen
Crabbé, Applied and environmental microbiology 2011 - “...PA5049 PA5054 PA5067 PA5069 PA5078 PA5117 PA5128 PA5276 PA5316 PA5355 PA5460 PA5490 PA5491 PA5555 PA5557 PA5569 PA5570 ispB glyA3 PA4608 PA4610 PA4633 PA4671...”
- Quorum-sensing antagonistic activities of azithromycin in Pseudomonas aeruginosa PAO1: a global approach
Nalca, Antimicrobial agents and chemotherapy 2006 - “...PA4605 PA4670 PA4671 PA4751 PA4764 PA4765 PA5130 PA5191 PA5316 PA5481 c PA5482 PA0139 d PA0586 PA0852 d,e PA1048 PA1244 PA1871e PA2031 PA2146c PA2171c PA2190...”
- Microarray analysis of global gene expression in mucoid Pseudomonas aeruginosa
Firoved, Journal of bacteriology 2003 - “...Ribosome modulation factor (rmf) ATP-binding protease component ClpA PA5316 PA3742 PA4261 PA4262 PA4267 PA4247 PA4744 PA3049 PA2620 4.4 2.7 2.3 2.4 2.2 2.3 2.1...”
8cd1X / Q9HTN8 8cd1X (see paper)
92% identity, 97% coverage
PP_5282 ribosomal protein L28 from Pseudomonas putida KT2440
90% identity, 100% coverage
- H-NS Family Proteins Drastically Change Their Targets in Response to the Horizontal Transfer of the Catabolic Plasmid pCAR1
Nakamura, Frontiers in microbiology 2020 - “...D -Tyrosyl-tRNA(Tyr) deacylase PP_5087 rpmE 50S ribosomal protein L31 PP_5281 rpmG 50S ribosomal protein L33 PP_5282 rpmB 50S ribosomal protein L28 Next, we sorted the differentially transcribed genes in KT2440 turA (pCAR1) and KT2440 turB (pCAR1) in the stationary phase into the COG categories ( Figure...”
- “...S18 PP_4877 rpsF a 30S ribosomal protein S6 PP_5087 rpmE a 50S ribosomal protein L31 PP_5282 rpmB a,c 50S ribosomal protein L28 a Down-regulated genes by the deletion of turA in KT2440(pCAR1) during the log phase. b Up-regulated genes by the deletion of turA in KT2440(pCAR1)...”
P0A2A5 Large ribosomal subunit protein bL28 from Salmonella typhimurium (strain LT2 / SGSC1412 / ATCC 700720)
STM3728 50S ribosomal subunit protein L28 from Salmonella typhimurium LT2
SEN3550 50S ribosomal subunit protein L28 from Salmonella enterica subsp. enterica serovar Enteritidis str. P125109
SENTW_3829 50S ribosomal protein L28 from Salmonella enterica subsp. enterica serovar Weltevreden str.
86% identity, 99% coverage
RpmB / b3637 50S ribosomal subunit protein L28 from Escherichia coli K-12 substr. MG1655 (see 39 papers)
rpmB / P0A7M2 50S ribosomal subunit protein L28 from Escherichia coli (strain K12) (see 35 papers)
RL28_ECOLI / P0A7M2 Large ribosomal subunit protein bL28; 50S ribosomal protein L28 from Escherichia coli (strain K12) (see 7 papers)
rpmB / RF|NP_418094 50S ribosomal protein L28 from Escherichia coli K12 (see paper)
NP_418094 50S ribosomal subunit protein L28 from Escherichia coli str. K-12 substr. MG1655
b3637 50S ribosomal protein L28 from Escherichia coli str. K-12 substr. MG1655
NP_709416 50S ribosomal subunit protein L28 from Shigella flexneri 2a str. 301
c4461 50S ribosomal protein L28 from Escherichia coli CFT073
Z5061 50S ribosomal subunit protein L28 from Escherichia coli O157:H7 EDL933
ECs4512 50S ribosomal subunit protein L28 from Escherichia coli O157:H7 str. Sakai
BHE81_18145, Z_RS23800 50S ribosomal protein L28 from Klebsiella sp. AqSCr
84% identity, 99% coverage
- subunit: Part of the 50S ribosomal subunit.
- Primary structure of protein L28 from the large subunit of Escherichia coli ribosomes.
Wittmann-Liebold, FEBS letters 1977 (PubMed)- GeneRIF: N-terminus verified by Edman degradation on mature peptide
- Liquid-Liquid Phase Separation and Protective Protein Aggregates in Bacteria
Kuczyńska-Wiśnik, Molecules (Basel, Switzerland) 2023 - “...0.411 0.255 0.051 12 P0A7W7 30S ribosomal protein S8 1.09 2813 0.038 0.123 0.003 13 P0A7M2 50S ribosomal protein L28 1.00 4610 0.283 0.142 0.013 14 P0A7S9 30S ribosomal protein S13 1.00 6249 0.322 0.245 0.014 15 P0A7V8 30S ribosomal protein S4 0.96 2549 0.690 0.178...”
- Ionizing Radiation-induced Proteomic Oxidation in Escherichia coli
Bruckbauer, Molecular & cellular proteomics : MCP 2020 - “...TMT6plex [K11]; 1 TMT6plex [N-Term] 2.77 0.022 Ambiguous, likely W6 RpmB 50S ribosomal protein L28 P0A7M2 0.032 [R].F W VESEK.[R] 1xTrioxidation [W2]; 1 TMT6plex [K7]; 1 TMT6plex [N-Term] 2.22 0.049 OK RpsD 30S ribosomal protein S4 P0A7V8 0.070 [R]. M GFGATR.[A] 1xHydroxylation [M1]; 1 TMT6plex [N-Term]...”
- Capturing Membrane Protein Ribosome Nascent Chain Complexes in a Native-like Environment for Co-translational Studies
Pellowe, Biochemistry 2020 - “...RL20, P0A7L3; 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...”
- 5-azacytidine induces transcriptome changes in Escherichia coli via DNA methylation-dependent and DNA methylation-independent mechanisms
Militello, BMC microbiology 2016 - “...of catabolite repression; CRP; CAP 1.40 1.49E-04 b2796 sdaC L-serine:H+ symport permease, threonine-insensitive 1.40 1.84E-03 b3637 rpmB 50S ribosomal subunit protein L28 1.38 9.87E-05 b3508 yhiD Predicted Mg(2+) transport ATPase, MgtC family, function unknown; inner membrane protein 1.35 2.62E-03 b3339 tufA Translation elongation factor EF-Tu 1;...”
- Analysis of promoter targets for Escherichia coli transcription elongation factor GreA in vivo and in vitro
Stepanova, Journal of bacteriology 2007 - “...1.6 Involved in lipopolysaccharide biosynthesis rpmG rpmB b3636 b3637 2.4 2.6 50S ribosomal subunit protein L33 50S ribosomal subunit protein L28 rpmH rnpA...”
- Global gene expression profiling of the asymptomatic bacteriuria Escherichia coli strain 83972 in the human urinary tract
Roos, Infection and immunity 2006 - “...b2153 b0114 b3986 b0169 c4310 b4457 b3301 b2415 b3305 b3637 b1779 b3342 b3186 b3307 b4000 b0755 b3340 b3321 b1824 b3316 50S ribosomal subunit protein L5 5S rRNA...”
- YdgG (TqsA) controls biofilm formation in Escherichia coli K-12 through autoinducer 2 transport
Herzberg, Journal of bacteriology 2006 - “...rplK rplP rpmC b3320 b3317 b3318 b3321 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...”
- Combined, functional genomic-biochemical approach to intermediary metabolism: interaction of acivicin, a glutamine amidotransferase inhibitor, with Escherichia coli K-12
Smulski, Journal of bacteriology 2001 - “...xseA ygiC yjjR yjjS yjjT zwf b3318 b3309 b2185 b3185 b3637 b3302 b3636 b3703 b3299 b3295 b3314 b3296 b3303 b4200 b3341 b3306 b3230 b3321 b3297 b3298 b3307 b2609...”
- Genome-wide transcriptional profiling of the Escherichia coli responses to superoxide stress and sodium salicylate
Pomposiello, Journal of bacteriology 2001 - “...b3301 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...”
- 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 L23 Cytoplasm No Hits 13 NP_709097 50S ribosomal 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...”
- The Engineered Lysin CF-370 Is Active Against Antibiotic-Resistant Gram-Negative Pathogens In Vitro and Synergizes With Meropenem in Experimental Pseudomonas aeruginosa Pneumonia
Sauve, The Journal of infectious diseases 2024 (secret) - Lipid-Functionalized Single-Walled Carbon Nanotubes as Probes for Screening Cell Wall Disruptors
Kallmyer, ACS applied materials & interfaces 2023 (secret) - In Vitro Potency and Spectrum of the Novel Polymyxin MRX-8 Tested against Clinical Isolates of Gram-Negative Bacteria
Duncan, Antimicrobial agents and chemotherapy 2022 (secret) - Transcriptional responses of Escherichia coli K-12 and O157:H7 associated with lettuce leaves
Fink, Applied and environmental microbiology 2012 - “...Z4678 Z4675 Z5556 Z4589 Z4680 Z4674 Z4689 Z4679 Z3444 Z5061 Z5060 Z5194 Z0180 Z4666 Z4673 Z5809 Z4676 Z4692 Z4667 Z4700 Z4668 Z4677 Z4526 Z3903 Z5811 Z0027...”
- Global transcriptional response of Escherichia coli O157:H7 to growth transitions in glucose minimal medium
Bergholz, BMC microbiology 2007 - “...lldP 2.39 2 ECs3463 tyrA 3.67 3 ECs4490 gpmI -3.35 1 ECs3464 aroF 3.30 3 ECs4512 rpmB -2.38 1 ECs3471 yfjA -3.58 1 ECs4553 O157 -2.10 1 ECs3546 emrR -3.47 1 ECs4575 escC -2.00 1 ECs3559 srlA_1 2.08 3 ECs4632 yidA -2.02 1 ECs3595 rpoS 2.80...”
- Transcriptome Analysis Reveals Cr(VI) Adaptation Mechanisms in Klebsiella sp. Strain AqSCr
Lara, Frontiers in microbiology 2021 - “...encoding ribosomal subunits S9 (BHE81_16380), S21 (BHE81_15345), S22 (BHE81_15345), L13 (BHE81_16385), L27 (BHE81_16205), and L28 (BHE81_18145) were upregulated ( Supplementary Table 5 ), while ycfD (BHE81_25675), encoding a putative hydroxylase of the 50S ribosomal protein L16, was downregulated ( Supplementary Table 6 ) with respect to...”
- Transcriptomic Analysis of Viable but Non-Culturable Escherichia coli O157:H7 Formation Induced by Low Temperature
Zhong, Microorganisms 2019 - “...Genes in the Signal Pathway Ko03010 Ribosome rps O, rpl S, rps M, rpl F, Z_RS23800, rpl T, rps Q, rps R, rps D, rps B, rpl U, Z_RS08020, rpl B, rpl R, rpl D, rpl V, Z_RS16205, rps C, rpl C, rpl W, rpmC ,...”
VP0185 ribosomal protein L28 from Vibrio parahaemolyticus RIMD 2210633
81% identity, 100% coverage
8a3lw / P0A7M2 8a3lw (see paper)
84% identity, 97% coverage
8rd8WD / A0A0M4T6Y7 8rd8WD (see paper)
83% identity, 97% coverage
BB3371 50S ribosomal protein L28 from Bordetella bronchiseptica RB50
78% identity, 100% coverage
VC0218 ribosomal protein L28 from Vibrio cholerae O1 biovar eltor str. N16961
79% identity, 100% coverage
- Mining regulatory 5'UTRs from cDNA deep sequencing datasets
Livny, Nucleic acids research 2010 - “...* VC2490 2-isopropylmalate synthase T-box(11), Leu leader(28), ydaO-yuaA(1) 21 VC0007 50S ribosomal protein L34 22 VC0218 Ribosomal protein L28 RLE0348 23 VC0324 50S ribosomal protein L11 RLE0241 , RLE0148(6) 24 VC2597 30S ribosomal protein S10 RLE0110(25) 25 VC2679 50S ribosomal protein L31 RLE0089(8) 26 VCA0166 Cold-shock...”
HSM_0010 50S ribosomal protein L28 from Haemophilus somnus 2336
HSM_0010 50S ribosomal protein L28 from Histophilus somni 2336
79% identity, 100% coverage
EAMY_0077 50S ribosomal protein L28 from Erwinia amylovora CFBP1430
81% identity, 99% coverage
FTH_0519 ribosomal protein L28 from Francisella tularensis subsp. holarctica OSU18
76% identity, 100% coverage
- Use of magnetic hydrazide-modified polymer microspheres for enrichment of Francisella tularensis glycoproteins
Horák, Soft matter 2012 - “...factor protein MinE 10.18/8.03 cyt cyt FTH_0516 Septum site-determining protein MinD 30.8/6.85 cyt, MLS cyt FTH_0519 Ribosomal protein L28 8.94/11.06 cyt cyt FTH_0535 DNA topoisomerase (ATP-hydrolyzing) 97.13/5.41 cyt cyt FTH_0539 UDP-3- O -[3-hydroxymyristoyl] glucosamine N -acyltransferase 35.8/5.80 cyt cyt FTH_0540 (3 R )-Hydroxymyristoyl-[acyl-carrier-protein] dehydratase 18.15/6.83 cyt...”
- “...factor protein MinE 10.18/8.03 cyt cyt FTH_0516 Septum site-determining protein MinD 30.8/6.85 cyt, MLS cyt FTH_0519 Ribosomal protein L28 8.94/11.06 cyt cyt FTH_0540 (3R)-Hydroxymyristoyl-[acyl-carrier-protein] dehydratase 18.15/6.83 cyt cyt FTH_0570 Putative uncharacterized protein 19.79/9.74 ? SPI FTH_0585 Acyl-CoA dehydrogenase 84.19/8.45 ? cyt FTH_0586 Long-chain-fatty-acidCoA ligase 63.07/7.57 CM...”
7uvxW 7uvxW (see paper)
AB57_0531 ribosomal protein L28 from Acinetobacter baumannii AB0057
ACIAD0502 50S ribosomal protein L28 from Acinetobacter sp. ADP1
A9801_RS02635 50S ribosomal protein L28 from Acinetobacter baumannii
76% identity, 100% coverage
- Ligands: rna; streptothricin f (7uvxW)
- The lytic transglycosylase MltB connects membrane homeostasis and in vivo fitness of Acinetobacter baumannii
Crépin, Molecular microbiology 2018 - “...transglycosylase 9.36 0.0000 AB57_2865 NUDIX hydrolase 9.24 0.0022 AB57_0530 50S ribosomal protein L33 9.24 0.0001 AB57_0531 50S ribosomal protein L28 9.24 0.0001 AB57_0459 hypothetical protein 9.21 0.0052 AB57_0336 glutamylQ tRNA(Asp) ligase 9.17 0.0000 AB57_3836 phosphoserine phosphatase 9.16 0.0035 AB57_2526 phosphoribosylamineglycine ligase 9.15 0.0001 AB57_3700 endonuclease 9.15...”
- iTRAQ-Based Comparative Proteomic Analysis of Acinetobacter baylyi ADP1 Under DNA Damage in Relation to Different Carbon Sources
Jiang, Frontiers in microbiology 2019 - “...50S ribosomal protein L33 rpmG ACIAD0501 0.45 0.77 0.33 0.4 50S ribosomal protein L28 rpmB ACIAD0502 0.52 0.65 0.39 0.53 30S ribosomal protein S12 rpsL ACIAD0881 0.37 0.49 0.3 0.51 BetI family transcriptional regulator betI ACIAD1010 0.67 0.69 0.81 0.63 DNA-binding ATP-dependent protease La lon ACIAD1115...”
- Characterization and Transcriptome Studies of Autoinducer Synthase Gene from Multidrug Resistant Acinetobacter baumannii Strain 863
Ng, Genes 2019 - “...A9801_RS14385; L11, A9801_RS03460; L13, A9801_RS15160; L14, A9801_RS14430; L17, A9801_RS14510; L23, A9801_RS14390; L25, A9801_RS05355 & L28, A9801_RS02635) were associated with the large subunit. Besides ribosomal proteins, ribosome maturation factor, rimM (A9801_RS13970) and ribosome recycling factor, rrf (A9801_RS10865) were also repressed in A. baumannii strain 863 abaI :Km....”
B7C60_RS05715 50S ribosomal protein L28 from Vibrio fujianensis
78% identity, 100% coverage
HI0951 ribosomal protein L28 (rpL28) from Haemophilus influenzae Rd KW20
78% identity, 100% coverage
A1JHR2 Large ribosomal subunit protein bL28 from Yersinia enterocolitica serotype O:8 / biotype 1B (strain NCTC 13174 / 8081)
79% identity, 99% coverage
BTH_I0780 ribosomal protein L28, putative from Burkholderia thailandensis E264
BCAL2714 50S ribosomal protein L28 from Burkholderia cenocepacia J2315
bglu_1g28680 50S ribosomal protein L28 from Burkholderia glumae BGR1
BPSL0916, bgla_1g32050 50S ribosomal protein L28 from Burkholderia multivorans
78% identity, 97% coverage
- Gene and protein expression in response to different growth temperatures and oxygen availability in Burkholderia thailandensis
Peano, PloS one 2014 - “...S20 4.59 2.2 All [33] BTH_I0779 ( rpmG ) L33 3.73 1.9 All rpmG rpmB BTH_I0780 ( rpmB ) L28 3.73 1.9 150 All rpmG rpmB BTH_I1055 ( rpsO ) S15P/S13E 2.30 1.2 All BTH_I1140 ( rplU ) L21 4.29 2.1 All rplU rpmA BTH_I1141 (...”
- Identification of small RNAs abundant in Burkholderia cenocepacia biofilms reveal putative regulators with a potential role in carbon and iron metabolism
Sass, Scientific reports 2017 - “...dual nature: 5end of long mRNA and sRNA. ncS18 was co-regulated with its downstream gene (BCAL2714) across four growth conditions (Fig. S2 ), while ncS33 was differentially regulated from its downstream gene (BCAM1726, Fig. S2 ). Figure 3 RACE analysis of two processed 5UTRs, ncS33 (top)...”
- “...ribonuclease E 34 (BCAL2888), a proline-betaine transporter 35 (BCAL1252), ribosomal proteins 36 (BCAL0115, BCAL2091, BCAL2765, BCAL2714, BCAL3348), carA 37 (BCAL1260) and tRNA-synthetases 36 (BCAL3373, BCAL3436). Attenuation, observed for many short 5UTRs, is indicative of a cis-regulatory function. Overall, 5UTRs of B. cenocepacia are an abundant source...”
- Genome-wide transcription start site profiling in biofilm-grown Burkholderia cenocepacia J2315
Sass, BMC genomics 2015 - “...208 yes BCAL2293 BCAL2294 Complement (2545296..2545503) 1 RNA-Seq[ 36 ] ncS18 + 178 no BCAL2713 BCAL2714 2979006..2979183 1 RNA-Seq[ 36 ] ncS21 a + 361 yes BCAL2737 BCAL2738 3008232..3008591 1 RNA-Seq[ 36 ] ncS33 + 93 no BCAM1725 BCAM1726 1926664..1926756 2 RNA-Seq[ 36 ] ncS36 +...”
- Computational Identification and Comparative Analysis of Secreted and Transmembrane Proteins in Six Burkholderia Species
Nguyen, The plant pathology journal 2017 - “...strains Protein name Definition Locus ID B. glumae BGR1 WP_004186391.1 MS: 50S ribosomal protein L28 bglu_1g28680 WP_012734522.1 FMN-dependent NADH-azoreductase bglu_1g04330 WP_012734950.1 Cytidylate kinase bglu_1g08790 WP_015875283.1 ABC transporter bglu_1g12300 WP_015875291.1 AraC family transcriptional regulator bglu_1g12380 WP_012734097.1 Sigma-54-dependent Fis family transcriptional regulator bglu_1p1190 WP_012733828.1 AraC family transcriptional regulator...”
- RNAseq-based Transcriptome Analysis of Burkholderia glumae Quorum Sensing
Kim, The plant pathology journal 2013 - “...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 rplY 1.1 0.7 0.8 0.9 bglu_2g15900 rpsU 0.5 0 1.5 1.1 1...”
- Unraveling the role of toxin-antitoxin systems in <i>Burkholderia pseudomallei</i>: exploring bacterial pathogenesis and interactions within the HigBA families
Chapartegui-González, Microbiology spectrum 2024 - “...many genes that encode for proteins related to ribosomal functions (BPSL1458, BPSL1460, BPSL1461, BPSL1491, BPSL0915, BPSL0916, BPSL0871, BPSL1355, BPSL1206, BPSL1511, BPSL0520, and BPSL0075a) were identified. When the different strains were exposed to ciprofloxacin, the double mutants lacking the whole TA system exhibited reduced survival compared with...”
- Computational Identification and Comparative Analysis of Secreted and Transmembrane Proteins in Six Burkholderia Species
Nguyen, The plant pathology journal 2017 - “...bgla_2g29570 B. pseudomallei K96243 YP_106977.1 Fis family transcriptional regulator BPSL0350 YP_107543.1 50S ribosomal protein L28 BPSL0916 YP_108790.1 AraC family transcriptional regulator BPSL2195 YP_109070.1 Sigma-54 dependent regulatory protein BPSL2475 YP_109112.1 Cytidylate kinase BPSL2516 YP_109327.1 AraC family transcriptional regulator BPSL2731 YP_109651.1 ACP phosphodiesterase BPSL3056 YP_110488.1 Putrescine ABC transporter...”
- “...transcriptional regulator bgla_1g15580 WP_013698566.1 AraC family transcriptional regulator bgla_1g26190 WP_004186391.1 MS: 50S ribosomal protein L28 bgla_1g32050 WP_013690079.1 MS: alkyl hydroperoxide reductase subunit C bgla_2g13050 WP_013690224.1 Protocatechuate 3,4-dioxygenase subunit beta bgla_2g14510 WP_013691065.1 MS: hypothetical protein bgla_2g23080 WP_013691078.1 ABC transporter bgla_2g23220 WP_013691620.1 MS: alkyl hydroperoxide reductase subunit C...”
Bphyt_3149 50S ribosomal protein L28 from Burkholderia phytofirmans PsJN
76% identity, 97% coverage
Rmet_2870 50S ribosomal protein L28 from Cupriavidus metallidurans CH34
75% identity, 97% coverage
NGO1680 RpmB from Neisseria gonorrhoeae FA 1090
Q5F682 Large ribosomal subunit protein bL28 from Neisseria gonorrhoeae (strain ATCC 700825 / FA 1090)
76% identity, 97% coverage
lpg0479 50S ribosomal protein L28 from Legionella pneumophila subsp. pneumophila str. Philadelphia 1
72% identity, 100% coverage
- Transcriptomic changes of Legionella pneumophila in water
Li, BMC genomics 2015 - “...3.37 3.21 50S ribosomal protein L16 lpg0336 rplP 2.49 3.73 3.21 50S ribosomal protein L28 lpg0479 rpmB 2.00 2.89 3.40 50S ribosomal protein L6 lpg0344 rplF 2.49 3.81 3.47 Translation elongation factor G lpg0326 fusA 2.45 2.59 Translation elongation factor Ts lpg1713 tsf 1.40 1.20 Translation...”
XC_4123 50S ribosomal protein L28 from Xanthomonas campestris pv. campestris str. 8004
76% identity, 100% coverage
PD0488 50S ribosomal protein L28 from Xylella fastidiosa Temecula1
76% identity, 100% coverage
MSMEG_6068 ribosomal protein L28 from Mycobacterium smegmatis str. MC2 155
55% identity, 100% coverage
- Critical Role of Zur and SmtB in Zinc Homeostasis of Mycobacterium smegmatis
Goethe, mSystems 2020 - “...protein S14 rpmG MSMEG_6067 Rv2057c (87.0) MAP3769c (92.6) <0.0001 1,043.5 50S ribosomal protein L33 rpmB MSMEG_6068 Rv2058c (82.1) <0.0001 449.65 50S ribosomal protein L28 MSMEG_6069 Rv0106 (62.1) MAP3770 (57.8) <0.0001 406.31 (4,524.0) CobW/P47K domain-containing protein, MPY recruitment factor (MRF) rpmE2 MSMEG_6070 MAP3771 (79.3) <0.0001 1,233.0 50S...”
- “...encoding zinc-independent alternative ribosomal proteins (ARPs) RpsR, RpsN, RpmG, RpmB, and RpmE2 (MSMEG_6065, MSMEG_6066, MSMEG_6067, MSMEG_6068, MSMEG_6070), a gene encoding the porin MspD (MSMEG_6057), and two genes of unknown function (MSMEG_6055, MSMEG_6064). In addition, 7-fold-lower expression upon TPEN treatment was observed for the cobalt-zinc-cadmium resistance gene...”
- Adaptation of mycobacteria to growth conditions: a theoretical analysis of changes in gene expression revealed by microarrays
Cox, PloS one 2013 - “...slower growth rate (see below and Figs. 1b and 1c ). Those ORFs (MSMEG_6065 to MSMEG_6068) encoding the subset of ribosomal proteins regulated by Zur were found to have r -values in the range 0.851.15 compared with the up regulation of the orthologous ORFs (BCG_2074c BCG_2077c)...”
- Gene Expression, Bacteria Viability and Survivability Following Spray Drying of Mycobacterium smegmatis
Lauten, Materials (Basel, Switzerland) 2010 - “...L25, Ctc-form 1.9 11.3 0.000 99% MSMEG_4624 ribosomal protein L27 rpmA 0.2 12.9 0.324 0% MSMEG_6068 ribosomal protein L28 rpmB 0.1 9.8 0.734 0% MSMEG_2400 ribosomal protein L28 rpmB 1.5 12.8 0.000 99% MSMEG_1444 ribosomal protein L29 rpmC 1.8 11.8 0.013 14% MSMEG_1473 ribosomal protein L30...”
SCO3429 50S ribosomal protein L28 from Streptomyces coelicolor A3(2)
46% identity, 100% coverage
- The frontline antibiotic vancomycin induces a zinc starvation response in bacteria by binding to Zn(II)
Zarkan, Scientific reports 2016 - “...in S. coelicolor ( b ) the putative Zur regulated genes SGR5019 (SCO2505 orthologue), SGR0545 (SCO3429 orthologue) and SGR0546 (SCO3428 orthologue) in S. griseus ( c ) the putative Zur regulated genes SSGG01683 (SCO2505 orthologue), SSGG00253 (SCO0476 orthologue) and SSGG06641 (SCO3428 orthologue) in S. roseosporus (...”
- Comparative genomics of Streptomyces avermitilis, Streptomyces cattleya, Streptomyces maritimus and Kitasatospora aureofaciens using a Streptomyces coelicolor microarray system
Hsiao, Antonie van Leeuwenhoek 2008 - “...L31 0.24 0.37 0.22 0.60 SCO3428 putative 50S ribosomal protein L33 0.15 0.28 0.54 0.09 SCO3429 putative 50S ribosomal protein L28 0.68 0.16 0.55 0.45 SCO3430 putative 30S ribosomal protein S14 0.80 0.10 0.17 0.19 SCO3880 putative 50S ribosomal protein L34 1.02 0.13 0.24 0.71 SCO3906...”
- Zinc-responsive regulation of alternative ribosomal protein genes in Streptomyces coelicolor involves zur and sigmaR
Owen, Journal of bacteriology 2007 - “...rpmJ1 (SCO4726) rpsN2 (SCO3430) rpsR2 (SCO3425) rpmB2 (SCO3429) rpmE2 (SCO3427) rpmE3 (SCO1150) rpmF2 (SCO0436) rpmG2 (SCO3428) rpmG3 (SCO0570) rpmJ2 (SCO0569)...”
- The zinc-responsive regulator Zur controls a zinc uptake system and some ribosomal proteins in Streptomyces coelicolor A3(2)
Shin, Journal of bacteriology 2007 - “...within the intergenic regions of rpmG2 (SCO3428) and rpmB2 (SCO3429), it is very likely that rpmB2, encoding a C paralogue of L28, is also regulated by Zur,...”
TW113, TWT113 50S ribosomal protein L28 from Tropheryma whipplei str. Twist
51% identity, 100% coverage
RSP_2016 50S ribosomal protein L28 from Rhodobacter sphaeroides 2.4.1
49% identity, 75% coverage
AS87_06160 50S ribosomal protein L28 from Riemerella anatipestifer Yb2
52% identity, 83% coverage
Fjoh_4983 ribosomal protein L28 from Flavobacterium johnsoniae UW101
49% identity, 96% coverage
C9Z0W7 Large ribosomal subunit protein bL28 from Streptomyces scabiei (strain 87.22)
46% identity, 92% coverage
BT_0916 50S ribosomal protein L28 from Bacteroides thetaiotaomicron VPI-5482
41% identity, 87% coverage
CJJ81176_0475 ribosomal protein L28 from Campylobacter jejuni subsp. jejuni 81-176
Cj0450c 50S ribosomal protein L28 from Campylobacter jejuni subsp. jejuni NCTC 11168
55% identity, 79% coverage
- Campylobacter jejuni Virulence Factors Identified by Modulating Their Synthesis on Ribosomes With Altered rRNA Methylation
Sałamaszyńska-Guz, Frontiers in cellular and infection microbiology 2021 - “...Uncharacterized protein CJJ81176_1344 Preprotein translocase, YajC CJJ81176_1112 Para protein, Cjp26 CJJ81176_pVir0025 50S ribosomal protein L28 CJJ81176_0475 Tryptophan synthase alpha chain, TrpA CJJ81176_0373 Putative sugar transferase CJJ81176_1435 Carbon starvation protein A, CstA CJJ81176_0924 Cytolethal distending toxin, subunit C, CdtC CJJ81176_0114 Flagellar P-ring protein, FlgI CJJ81176_1455 Protein TonB...”
- Transcriptomic analysis of Campylobacter jejuni NCTC 11168 in response to epinephrine and norepinephrine
Xu, Frontiers in microbiology 2015 - “...all up-regulated by Epi or NE. Moreover, genes of rpsU ( Cj0370 ), rpmB ( Cj0450c ), rplO-rpsE ( Cj1690c-Cj1689c ) increased in expression by Epi and rpsD ( Cj1594 ) increased in expression by NE. Genes with opposite expression patterns between catecholamines and iron Notably,...”
YSS_RS02020 50S ribosomal protein L28 from Campylobacter coli RM4661
53% identity, 79% coverage
- Proteotyping as alternate typing method to differentiate Campylobacter coli clades
Emele, Scientific reports 2019 - “...YSS_RS02145 RpmG/L33 AGCTGATGGCGTTGAAATGG ACCCCCAACCATCGGATTTG 430 YSS_RS09385 RpsN/S14 ACACGACGACCTGGTTTAGA TCGGTCTTGATGAGCAGTTGA 611 YSS_RS09410 RpmC/L29 GGTCTGCATTCAACCGCTAC GCCAAATTGAAGCAGCTCGT 668 YSS_RS02020 RpmB/L28 CGTCAAGTTCATTATGGCGCT TGGAACAAAATGCCCGTCCA 742 YSS_RS08275 RpmI/L35 GCAAGCAGCATTGATACGCA GCTTGGCTATTTTGCAAAGGATT 715 YSS_RS08510 RpmE/L31 GCAAGGTTTTTCCTGATGCTGT TGGCATACCCGCATCACTC 756 YSS_RS09395 RplX/L24 TCGGAACTCGTATCTTTGGGC CAGGAAAACCTTCACGCACT 578 YSS_RS02035 DUF465 GCTGCTGGGTAAGATTTTGGT TCGTGTAACCCTAGAAGATGGC 584 YSS_RS00440 RpmA/L27 AGTTAGCGTTGGCGATGAGTT AACGAAGATGATATCCCCGCC 783 YSS_RS00790...”
MAB_0334c 50S ribosomal protein L28-2 from Mycobacterium abscessus ATCC 19977
48% identity, 94% coverage
- 2-Aminoimidazoles Inhibit Mycobacterium abscessus Biofilms in a Zinc-Dependent Manner
Belardinelli, International journal of molecular sciences 2022 - “...an asterisk. Similarly colored genes denote gene clusters likely to be cotranscribed. MAB_0331c, MAB_0332c, MAB_0333c, MAB_0334c and MAB_0336 are Zn-independent alternative ribosomal proteins. MAB_0335 is likely to be involved in cobalamin biosynthesis. MAB_0575c-MAB_0576c-MAB_0577c encode a putative zinc importer of the ABC-transporter family. The operon encompassing genes...”
- “...30S ribosomal protein S14 RpsN2 7.76 8.93 MAB_0333c 50S ribosomal protein L33 RpmG1 9.72 6.26 MAB_0334c * 50S ribosomal protein L28 RpmB2 9.30 7.83 MAB_0335 * Probable cobalamin synthesis protein Cobalamin biosynthesis 7.95 10.46 MAB_0336 50S ribosomal protein L31 type B Zn-independent ribosomal protein 8.52 9.38...”
BMEI0056 LSU ribosomal protein L28P from Brucella melitensis 16M
Q2YR56 Large ribosomal subunit protein bL28 from Brucella abortus (strain 2308)
BAB1_2016 Ribosomal protein L28:ATP/GTP-binding site motif A (P-loop) from Brucella melitensis biovar Abortus 2308
52% identity, 70% coverage
SMc00704 PROBABLE 50S RIBOSOMAL PROTEIN L28 from Sinorhizobium meliloti 1021
52% identity, 71% coverage
7jilX / A0A1B2U1R1 7jilX (see paper)
47% identity, 95% coverage
5mmiY / P82245 Structure of the large subunit of the chloroplast ribosome (see paper)
49% identity, 83% coverage
RK28_SPIOL / P82245 Large ribosomal subunit protein bL28c; 50S ribosomal protein L28, chloroplastic; CL28 from Spinacia oleracea (Spinach) (see 2 papers)
49% identity, 44% coverage
- function: Component of the chloroplast ribosome (chloro-ribosome), a dedicated translation machinery responsible for the synthesis of chloroplast genome-encoded proteins, including proteins of the transcription and translation machinery and components of the photosynthetic apparatus.
subunit: Component of the chloroplast large ribosomal subunit (LSU). Mature 70S chloroplast ribosomes of higher plants consist of a small (30S) and a large (50S) subunit. The 30S small subunit contains 1 molecule of ribosomal RNA (16S rRNA) and 24 different proteins. The 50S large subunit contains 3 rRNA molecules (23S, 5S and 4.5S rRNA) and 33 different proteins.
MT2118 50S ribosomal protein L28 from Mycobacterium tuberculosis CDC1551
BCG_2077c ribosomal protein L28 from Mycobacterium bovis BCG str. Pasteur 1173P2
Rv2058c 50S ribosomal protein L28 from Mycobacterium tuberculosis H37Rv
47% identity, 100% coverage
- The pup-proteasome system of Mycobacterium tuberculosis
Samanovic, Sub-cellular biochemistry 2013 - “...in translation 2.43 4.21 MT2117.1 Rv2057c rpmG1 Probable ribosomal L33. Involved in translation 2.91 4.2 MT2118 Rv2058c rpmB2 Probable 50S ribosomal protein L28. Involved I ribosome activity 3.47 6.12 MT2119 Rv2059 Conserved hypothetical protein. Unknown function n.i 2.17 MT2428 Rv2359 zur Zinc uptake regulator (formally furB...”
- Conserved codon composition of ribosomal protein coding genes in Escherichia coli, Mycobacterium tuberculosis and Saccharomyces cerevisiae: lessons from supervised machine learning in functional genomics
Lin, Nucleic acids research 2002 - “...MT2518, MT0733, MT0730, MT0741.1, MT2517, MT3052.2, MT2118, MT0114, MT0736, MT0728, MT0747, MT1337, MT2117.1, MT0663, MT4041.1, MT1680, MT3567.1, MT0729,...”
- Adaptation of mycobacteria to growth conditions: a theoretical analysis of changes in gene expression revealed by microarrays
Cox, PloS one 2013 - “...-values in the range 0.851.15 compared with the up regulation of the orthologous ORFs (BCG_2074c BCG_2077c) of BCG-Pasteur ( Table S1 ). We have yet to find an explanation for the different responses of these Zur-regulated genes comparing the two species. 2.4 Expression ratios of ORFs...”
- Exploring the manganese-dependent interaction between a transcription factor and its corresponding DNA: insights from gas-phase electrophoresis on a nES GEMMA instrument
Leščić, Analytical and bioanalytical chemistry 2024 - “...MMntR consensus binding sequence [ 28 ]. These sequences correspond to promoter regions for mntH (Rv2058c) and ABC transporter gene (Rv1283c), both involved in manganese transport in cells. In contrast to BMntR which exhibited binding to its target DNA molecule (Fig. 3 A), MMntR failed to...”
- “...(Fig. 3 C). It seems that changes at the beginning of DNA sequence (as in Rv2058c) as well as spread out changes (as in Rv1283c), in comparison to the consensus sequence [ 28 ] both diminish affinity of MMntR-DNA binding. However, especially for the latter, EMSA...”
- The efflux pumps Rv1877 and Rv0191 play differential roles in the protection of Mycobacterium tuberculosis against chemical stress
Sao, Frontiers in microbiology 2024 - “...protein L33 RpmG1 6.92 0.0114 rv2780 Secreted L-alanine dehydrogenase Ald (40kDa antigen; TB43) 6.78 0.0432 rv2058c 50S ribosomal protein L28 RpmB2 6.20 0.0014 rv3503c Probable ferredoxin FdxD 6.16 0.0068 rv0282 ESX conserved component EccA3. ESX-3 type VII secretion system protein. 5.89 0.0245 rv2628 Hypothetical protein 5.74...”
- “...TetR-family) 4.9 1.3E-02 rv0285 PE family protein PE5 4.7 rv0191 relative to the wild-type 0.0283 rv2058c 50S ribosomal protein L28 RpmB2 7.35 0.0281 rv2057c 50S ribosomal protein L33 RpmG1 6.49 0.0461 rv2056c 30S ribosomal protein S14 RpsN2 5.59 0.0291 rv0280 PPE family protein PPE3 5.54 0.0058...”
- Zinc limitation triggers anticipatory adaptations in Mycobacterium tuberculosis
Dow, PLoS pathogens 2021 - “...in ZLM vs. ZRM. H37Rv Locus Gene name Product (Protein name) logFC RNA logFC Protein Rv2058c rpmB2 50S ribosomal protein L28 (L28-2) 7.24 4.83 Rv0106 Rv0106 Conserved hypothetical protein 6.32 5.26 Rv0967 csoR Copper-sensitive operon repressor (CsoR) 4.58 4.32 Rv0969 ctpV Probable metal cation transporter P-type...”
- A Phenotypic Characterization of Two Isolates of a Multidrug-Resistant Outbreak Strain of Mycobacterium tuberculosis with Opposite Epidemiological Fitness
Bei, BioMed research international 2020 - “...(Rv3221c and Rv2081c), a GCN5-related N-acetyltransferase (Eis, Rv2416c), and a putative ribonuclease E (Rv2444c). Rv2057c, Rv2058c, Rv2154c, and Rv0290 showed a higher accumulation in Mp. Rv2057c and Rv2058c are ribosomal proteins, whereas Rv2154c is the peptidoglycan glycosyltransferase FtsW, which seems to participate in the peptidoglycan synthesis...”
- “...strain. In accordance with this conclusion, Mp accumulated higher amounts of proteins involved in translation (Rv2058c and Rv2057c) and cell division (FstW), whereas 410 overexpressed Rv1738, a protein likely involved in the shutdown of the ribosomal protein synthesis of M. tuberculosis induced under nitrosative and hypoxia...”
- Critical Role of Zur and SmtB in Zinc Homeostasis of Mycobacterium smegmatis
Goethe, mSystems 2020 - “...S14 rpmG MSMEG_6067 Rv2057c (87.0) MAP3769c (92.6) <0.0001 1,043.5 50S ribosomal protein L33 rpmB MSMEG_6068 Rv2058c (82.1) <0.0001 449.65 50S ribosomal protein L28 MSMEG_6069 Rv0106 (62.1) MAP3770 (57.8) <0.0001 406.31 (4,524.0) CobW/P47K domain-containing protein, MPY recruitment factor (MRF) rpmE2 MSMEG_6070 MAP3771 (79.3) <0.0001 1,233.0 50S ribosomal...”
- “...MSMEG_6067 Rv2057c (87.0) MAP3769c (92.6) 1.00 5856.67 1043.50 5,015.0 50S ribosomal protein L33 rpmB *MSMEG_6068 Rv2058c (82.1) 1.00 5372.69 449.65 4,055.32 50S ribosomal protein L28 *MSMEG_6069 Rv0106 (62.1) MAP3770 (57.8) 1.00 3492.00 406.31 4,340.00 CobW/P47K domain-containing protein rpmE2 MSMEG_6070 MAP3771 (79.3) 1.00 1460.33 1233.00 1,603.0 50S...”
- Role of VapBC12 Toxin-Antitoxin Locus in Cholesterol-Induced Mycobacterial Persistence
Talwar, mSystems 2020 - “...and phages 100 Rv1316c Information pathways 60 Rv2069 Information pathways 60 Rv2906c Information pathways 60 Rv2058c Information pathways 66.66666667 Rv2056c Information pathways 66.66666667 Rv1643 Information pathways 66.66666667 Rv0722 Information pathways 100 Rv2441c Information pathways 100 Rv3053c Information pathways 100 Rv3462c Information pathways 100 Rv1772 Conserved hypotheticals...”
- Protein tyrosine kinase, PtkA, is required for Mycobacterium tuberculosis growth in macrophages
Wong, Scientific reports 2018 - “...secretion-associated protein 2.24 0.705 3.18 Zur Rv0106 1 Hypothetical protein 1.036 0.701 1.48 Zur RpmB2 (Rv2058c) 50S ribosomal protein L28 1.41 0.26 5.42 Zur RpmG1 (Rv2057c) 50S ribosomal protein L33 1.053 0.367 2.87 Zur RpsR2 (Rv2055c) 30S ribosomal protein S18 0.895 0.529 1.69 Zur RsmI (Rv1003)...”
- Identification of Mycobacterial Ribosomal Proteins as Targets for CD4+ T Cells That Enhance Protective Immunity in Tuberculosis
Kennedy, Infection and immunity 2018 - “...(Rv0640, Rv0652, Rv0682, Rv0683, Rv0700, Rv0701, Rv0707, Rv0714, Rv2058c, and Rv2904) (Fig. 1 and additional data not shown) were analyzed in silico for...”
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PG1960 ribosomal protein L28 from Porphyromonas gingivalis W83
PGN_1891 50S ribosomal protein L28 from Porphyromonas gingivalis ATCC 33277
F452_RS0102540, HMPREF1322_RS07695 50S ribosomal protein L28 from Porphyromonas gulae DSM 15663
45% identity, 95% coverage
- Microarray analysis of the transcriptional responses of Porphyromonas gingivalis to polyphosphate
Moon, BMC microbiology 2014 - “...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 PG2140 Ribosomal protein L32 3.40 PG0205 Peptide chain release factor 3 1.50 a Locus number, putative identification, and cellular role...”
- Role of the Porphyromonas gingivalis extracytoplasmic function sigma factor, SigH
Yanamandra, Molecular oral microbiology 2012 - “...PG0928, and PG0121). Finally, genes encoding stress response mechanisms such chaperones (PG0520-21) and ribosomal proteins (PG1960, PG0656, PG1959) were upregulated in V2948. The microarray data was validated by RNAseq analysis. As shown in Supplemental Table S4 most genes detected as regulated in our microarray analysis were...”
- “...28.705630 0.000000 (1.1E-11) 12 PG1663 ABC transporter, ATP-binding protein 1.085281 2.121788 31.306825 0.000000 (4.2E-12) 12 PG1960 ribosomal protein L28 1.074119 2.105436 24.181677 0.000000 (6.9E-11) 12 PG1119 flavodoxin, putative 1.041524 2.058401 54.008493 0.000000 (1.1E-14) 12 PG1496 Hypothetical protein 1.039165 2.055038 10.057285 0.000001 12 PG0656 ribosomal protein L34...”
- Role of oxyR in the oral anaerobe Porphyromonas gingivalis
Diaz, Journal of bacteriology 2006 - “...PG1321 PG1116 PG0686 PG1540 PG1124 PG0257 PG0888 PG1089 PG1960 PG0385 PG0707 PG1076 PG0037 PG0595 PG2117 PG1134 PG1108 PG0594 PG0193 PG1542 PG0434 Alkyl...”
- Synthesis of ppGpp impacts type IX secretion and biofilm matrix formation in Porphyromonas gingivalis
Kim, NPJ biofilms and microbiomes 2020 - “...1.89 PGN_1869 rpsJ 30S ribosomal protein S10 1.86 PGN_1890 rpmG 50S ribosomal protein L33 1.99 PGN_1891 rpmB 50S ribosomal protein L28 2.17 Metabolic and biosynthetic process PGN_0024 ispF 2-C-methyl- d -erythritol 2,4-cyclodiphosphate synthase 2.17 PGN_0310 Uroporphyrinogen-III synthase 1.90 PGN_0532 Magnesium chelatase subunit I 1.88 PGN_0800 Electron...”
- Insights into Dynamic Polymicrobial Synergy Revealed by Time-Coursed RNA-Seq
Hendrickson, Frontiers in microbiology 2017 - “...1.05 1.13 PGN_1580 rpsU , putative 30S ribosomal protein S21 1.11 0.60 0.01 0.49 1.01 PGN_1891 rpmB , 50S ribosomal protein L28 0.18 0.22 0.44 0.33 0.92 PGN_2037 dps , DNA-binding protein from starved cells 1.14 0.84 1.02 1.31 0.78 a Results are expressed as log...”
- Pathway analysis for intracellular Porphyromonas gingivalis using a strain ATCC 33277 specific database
Hendrickson, BMC microbiology 2009 - “...PGN_1854 PGN_1588 PGN_1590 PGN_1855 PGN_1861 PGN_1832 PGN_1840 PGN_1863 PGN_1868 PGN_1842 PGN_1843 PGN_1872 PGN_1890 PGN_1849 PGN_1850 PGN_1891 PGN_1856 PGN_1857 PGN_1857 PGN_1858 PGN_1860 PGN_1862 PGN_1864 PGN_1865 PGN_1866 PGN_1867 PGN_1869 PGN_1871 Proteins are indicated as increased, decreased or unchanged in abundance for internalized P. gingivalis versus external control cells....”
- Hemin availability induces coordinated DNA methylation and gene expression changes in Porphyromonas gingivalis
Costeira, mSystems 2023 - “...flavoprotein subunit alpha/FixB family protein HMPREF1322_RS02075 76,668.23 2.38 0.25 7.17E-21 rpsO 30S ribosomal protein S15 HMPREF1322_RS07695 18,257.75 2.38 0.26 1.73E-20 50S ribosomal protein L28 HMPREF1322_RS07305 39,671.02 3.52 0.38 3.70E-20 SDR family oxidoreductase HMPREF1322_RS06590 3,693.30 2.34 0.26 7.00E-20 Lipoprotein signal peptidase HMPREF1322_RS04880 1,646.03 2.96 0.33 7.77E-20 Electron...”
- Hemin availability induces coordinated DNA methylation and gene expression changes in Porphyromonas gingivalis
Costeira, 2022 - Antibacterial effects of sodium tripolyphosphate against Porphyromonas species associated with periodontitis of companion animals
Lee, Journal of veterinary science 2019 - “...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 * F452_RS0106315 30S ribosomal protein S16 6.79E-15 +2.42 * F452_RS0105395 50S ribosomal protein L25 1.61E-12 +2.25...”
P30956 Large ribosomal subunit protein bL28c from Nicotiana tabacum
46% identity, 43% coverage
RPA0493 50S ribosomal protein L28 from Rhodopseudomonas palustris CGA009
49% identity, 73% coverage
- ATP Is a Major Determinant of Phototrophic Bacterial Longevity in Growth Arrest
Yin, mBio 2023 - “...light and dark-incubated conditions. From left to right, 50S ribosome: RPA0038, RPA0039, RPA0158, RPA0159, RPA0241, 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,...”
- Activity of the Rhodopseudomonas palustris p-coumaroyl-homoserine lactone-responsive transcription factor RpaR
Hirakawa, Journal of bacteriology 2011 - “...differentially expressed antisense transcripts (Table 2). The rpa0493 antisense transcript exhibited a 4- to 8-fold pC-HSL-RpaRdependent increase. This gene...”
- “...the 50S ribosomal subunit. The genes adjacent to rpa0493 did not show RpaR-pC-HSL regulation. Of particular interest was our observation that antisense reads...”
4v61BY 4v61BY (see paper)
46% identity, 83% coverage
CCNA_00699 LSU ribosomal protein L28P from Caulobacter crescentus NA1000
46% identity, 79% coverage
- The DEAD-box RNA helicase RhlB is required for efficient RNA processing at low temperature in Caulobacter
de, Microbiology spectrum 2023 - “...with four being upregulated (CCNA_02781, 02791, 03709, and 03973), and ten downregulated ( groES , CCNA_00699, 01585, 01770, 02273, 02341, 03371, 03587, 03666, and 03769) in the rhlB mutant. Six genes showed opposite expression profiles between temperatures (CCNA_00882, 02452, 03155, R0001, R0037, and R0058). It is...”
RK28_ARATH / O22795 Large ribosomal subunit protein bL28c; 50S ribosomal protein L28, chloroplastic; CL28 from Arabidopsis thaliana (Mouse-ear cress) (see paper)
AT2G33450 50S ribosomal protein L28, chloroplast (CL28) from Arabidopsis thaliana
46% identity, 45% coverage
- subunit: Part of the 50S ribosomal subunit.
disruption phenotype: Seedling lethality. Albino seedlings unable to grow under photoautotrophic conditions. - Membrane Proteomics of Arabidopsis Glucosinolate Mutants cyp79B2/B3 and myb28/29
Mostafa, Frontiers in plant science 2017 - “...Tair P49693 At4g02230 60S ribosomal protein L19-3 RPL19C 1.331 0.023 Translation and RNA binding Tair O22795 At2g33450 50S ribosomal protein L28 RPL28 1.331 0.032 Translation and RNA binding Tair Q9C514 At1g48830 40S ribosomal protein S7-1 RPS7A 1.327 0.031 Translation D Tair P49637 At1g70600 60S ribosomal protein...”
- Development of a Target Enrichment Probe Set for Conifer (REMcon)
Khan, Biology 2024 - “...1224 26 MA_10427590 AT1G17160 480 27 MA_10427203 AT2G36740 543 28 MA_10426631 AT4G36390 1533 29 MA_10426581 AT2G33450 231 30 MA_10426376 AT2G38270 504 31 MA_9578808 AT4G18372 387 32 MA_9514062 AT5G20220 315 33 MA_9503281 AT1G48175 257 34 MA_8815984 AT2G346401 693 35 MA_8715484 AT4G38020 501 36 MA_8687206 AT4G26980 408 37...”
- Phytochromes and Their Role in Diurnal Variations of ROS Metabolism and Plant Proteome
Luklová, International journal of molecular sciences 2022 - “...Col-0 and other phytochrome mutants included a decrease in the abundances of ribosomal proteins (AT1G18540, AT2G33450, AT4G31985, AT2G38140, and AT2G44120) and the sulfur assimilation enzyme ATP sulfurylase 2 (AT1G19920), and the accumulation of the multiple glutathione S-transferases mentioned above ( Table S1 ). Finally, the observed...”
- Arabidopsis CIA2 and CIL have distinct and overlapping functions in regulating chloroplast and flower development
Yang, Plant direct 2022 - “...PHYB (AT2G18790), PHYD (AT4G16250), PIF4 (AT2G43010), PKS4 (AT5G04190), RPS6 (AT4G31700), RPL11 (AT1G32990), RPL15 (AT3G25920), RPL28 (AT2G33450), RUP2 (AT5G23730), SEP2 (AT3G02310), SPA2 (AT4G11110), TOC33 (AT1G02280), TOC34 (AT5G05000), UBQ10 (AT4G05320), VRN2 (AT4G16845), and WOX1 (AT3G18010). 3 RESULTS 3.1 Partial functional redundancy between CIA2 and CIL That CIA2 and...”
- “...proteins (35) AT1G32990 50S ribosomal protein L11 (cpRPL11) 0.66 1.01 0.51 0.55 1.12 0.52 CP AT2G33450 50S ribosomal protein L28 (cpRPL28) 0.72 1.02 0.55 0.66 0.94 0.52 CP AT3G17170 30S ribosomal protein S6 (cpRPS6) 0.66 0.96 0.63 0.53 1.05 0.59 CP AT5G47190 50S ribosomal protein L192...”
- Plastid ribosome protein L5 is essential for post-globular embryo development in Arabidopsis thaliana
Dupouy, Plant reproduction 2022 - “...NA NA NA L27 Non-essential AT5G40950 Essential Romani et al. ( 2012 ) L28 Essential AT2G33450 Essential for greening process and post germination Romani et al. ( 2012 ) L29 Non-essential AT5G65220 NA NA L30 Non-essential NA NA NA L31 NA AT1G75350 Essential Hsu et al....”
- Integrated Transcriptional and Proteomic Profiling Reveals Potential Amino Acid Transporters Targeted by Nitrogen Limitation Adaptation
Liao, International journal of molecular sciences 2020 - “...RNA-binding protein cp31 2.59 0.001 5.50 0.004 At3g52380 RNA-binding protein cp33 2.78 0.003 4.46 0.003 At2g33450 chloroplast 50S ribosomal protein L28 3.27 0.001 5.32 0.001 At3g13120 chloroplast 30S ribosomal protein S10 3.75 0.002 6.71 0.003 At2g33450 chloroplast 50S ribosomal protein L28 4.20 0.001 7.45 0.001 At3g08740...”
- Separation and Paired Proteome Profiling of Plant Chloroplast and Cytoplasmic Ribosomes
Firmino, Plants (Basel, Switzerland) 2020 - “...NA AT5G54600 plastid 50S uL24c RPL24 + NA AT5G40950 plastid 50S bL27c RPL27 + NA AT2G33450 plastid 50S bL28c RPL28 + NA AT5G65220 plastid 50S uL29c RPL29 + NA AT1G75350 plastid 50S bL31c RPL31 + NA ATCG01020 plastid 50S bL32c RPL32 + NA AT2G24090 plastid 50S...”
- Spaceflight induces novel regulatory responses in Arabidopsis seedling as revealed by combined proteomic and transcriptomic analyses
Kruse, BMC plant biology 2020 - “...AT4G14250 Structural constituent of ribosome 2.66 0.001 AT3G13120 30S ribosomal protein S10, chloroplastic 1.00 0.015 AT2G33450 50S ribosomal protein L28, chloroplastic 1.01 0.021 AT5G30510 Ribosomal protein S1 1.01 0.002 AT5G54600 50S ribosomal protein L24, chloroplastic 1.01 0.012 AT1G79850 30S ribosomal protein S17, chloroplastic 1.02 0.002 AT5G20180...”
- Transcriptional analysis of sweet orange trees co-infected with 'Candidatus Liberibacter asiaticus' and mild or severe strains of Citrus tristeza virus
Fu, BMC genomics 2017 - “...L24, chloroplast (CL24) 1.98 RPL27 orange1.1g029509m AT5G40950 ribosomal protein large subunit 27 1.01 RPL28 orange1.1g031725m AT2G33450 50S ribosomal protein L28, chloroplast (CL28) 1.42 RPL29 orange1.1g030809m AT5G65220 ribosomal protein L29 family protein 1.32 RPL34 orange1.1g031306m AT1G29070 ribosomal protein L34 family protein 1.01 2.10 RPL35 orange1.1g031865m AT2G24090 ribosomal...”
- More
CT086 L28 Ribosomal Protein from Chlamydia trachomatis D/UW-3/CX
32% identity, 84% coverage
H375_5310 50S ribosomal protein L28 from Rickettsia prowazekii str. Breinl
48% identity, 65% coverage
Q5FFP1 Large ribosomal subunit protein bL28 from Ehrlichia ruminantium (strain Gardel)
ERGA_CDS_05500 50S ribosomal protein L28 from Ehrlichia ruminantium str. Gardel
41% identity, 74% coverage
RT0038 50S ribosomal protein L28 from Rickettsia typhi str. wilmington
46% identity, 65% coverage
- Genome-wide screen for temperature-regulated genes of the obligate intracellular bacterium, Rickettsia typhi
Dreher-Lesnick, BMC microbiology 2008 - “...1.1, 1.5) RT0870* 50S ribosomal protein L33 [Rickettsia typhi str. Wilmington] 2.3 (2.3, 1.9, 2.5) RT0038 50S ribosomal protein L28 [Rickettsia typhi str. Wilmington] 2.5 (4.1, 1.7, 1.3) RT0484 hypothetical protein RT0484 [Rickettsia typhi str. Wilmington] 1.6 (2.0, 1.6, 1.4) Replication, recombination and repair RT0339 exodeoxyribonuclease...”
B0JLJ8 Large ribosomal subunit protein bL28 from Microcystis aeruginosa (strain NIES-843 / IAM M-2473)
39% identity, 91% coverage
ssr1604 50S ribosomal protein L28 from Synechocystis sp. PCC 6803
39% identity, 90% coverage
HP0491 ribosomal protein L28 (rpL28) from Helicobacter pylori 26695
43% identity, 78% coverage
- Genome-wide association study of gastric cancer- and duodenal ulcer-derived Helicobacter pylori strains reveals discriminatory genetic variations and novel oncoprotein candidates
Tuan, Microbial genomics 2021 - “...[ 52 ], likely because of the high transcription of the upstream ribosome protein gene, HP0491. In a predicted secondary structure (M-fold) of the expected transcript, the discriminatory SNP was located at a loop-stem boundary, presumably slightly affecting interaction with a protein or an RNA. Use...”
- Use of Alignment-Free Phylogenetics for Rapid Genome Sequence-Based Typing of Helicobacter pylori Virulence Markers and Antibiotic Susceptibility
van, Journal of clinical microbiology 2015 - “...RpsT (HP0076), RpsI (HP0083), RplM (HP0084), RplT (HP0126), RpmF (HP0200), RplU (HP0296), RpmA (HP0297), RpmB (HP0491), RplI (HP0514), and RpmE (HP0551) amino acid sequences, followed by alignment and generation of phylogenetic trees with MEGA v5.2. FigTree ( http://tree.bio.ed.ac.uk/software/figtree/ ) was used for visualization of phylogenetic trees....”
- Comparison of genetic divergence and fitness between two subclones of Helicobacter pylori
Björkholm, Infection and immunity 2001 - “...type II HP0882, HP0085, JHP0165, JHP0956, HP0425 HP0491 HP0962 HP1192 rpL28, rpmB acpP NA JHP0726 hsdS_4 HP1382 HP1404 HP0062, HP0338, JHP0959,...”
YP_003057592 50S ribosomal subunit protein L28 from Helicobacter pylori B38
43% identity, 78% coverage
K9TX05 Large ribosomal subunit protein bL28 from Chroococcidiopsis thermalis (strain PCC 7203)
34% identity, 90% coverage
A8HWS8 Large ribosomal subunit protein bL28c from Chlamydomonas reinhardtii
34% identity, 35% coverage
BL0330 50S ribosomal protein L28 from Bifidobacterium longum NCC2705
46% identity, 73% coverage
Rv0105c PROBABLE 50S RIBOSOMAL PROTEIN L28-1 RPMB1 from Mycobacterium tuberculosis H37Rv
MT0114 ribosomal protein L28 from Mycobacterium tuberculosis CDC1551
44% identity, 63% coverage
- Label-Free Comparative Proteomics of Differentially Expressed Mycobacterium tuberculosis Protein in Rifampicin-Related Drug-Resistant Strains
Ullah, Pathogens (Basel, Switzerland) 2021 - “...unknown; probably involved in cellular metabolism. Probable oxidoreductase Intermediary metabolism and respiration RR and XDR Rv0105c rpmB Possibly involved in a translation mechanism 50S ribosomal protein L28-1 RpmB1 Information pathways RR and MDR Rv0282 eccA3 Unknown ESX conserved component EccA3. ESX-3 type VII secretion system protein....”
- Targeted RNA-Seq Reveals the M. tuberculosis Transcriptome from an In Vivo Infection Model
Cornejo-Granados, Biology 2021 - “...8 Rv0746 PE_PGRS9 PE-PGRS 4.35 10 4 9 Rv3345c PE_PGRS50 PE-PGR 1.94 10 4 10 Rv0105c uracil-DNA glycosylase 7.61 10 3 11 Rv2840c DUF448 domain-containing protein 6.94 10 3 12 Rv0440 molecular chaperone GroEL 5.71 10 3 13 Rv3620c peptidase M22 4.88 10 3 14 Rv0454...”
- Potential Genes Related to Levofloxacin Resistance in Mycobacterium tuberculosis Based on Transcriptome and Methylome Overlap Analysis
Li, Journal of molecular evolution 2020 - “...), php ( Rv0230c ), cyp132 ( Rv1394c ), pckA ( Rv0211 ), rpmB1 ( Rv0105c ), pfkB ( Rv2029c ), acg ( Rv2032 ), and ctpF ( Rv1997 ). In M. tuberculosis H37Rv, pgi ( Rv0946c ) encodes a protein belonging to glucose-6-phosphate isomerase, which...”
- Regulation of the CRISPR-Associated Genes by Rv2837c (CnpB) via an Orn-Like Activity in Tuberculosis Complex Mycobacteria
Zhang, Journal of bacteriology 2018 - “...Rv1808 Rv0768 Rv1168c Rv3054c Rv0251c Rv0331 Rv1169c Rv0105c Rv2010 Rv3174 Rv3615c Rv1130 Rv1554 Rv0384c Rv2025c Rv1286 Rv1805c Rv3614c Rv1552 Rv3616c Rv1809...”
- MntR(Rv2788): a transcriptional regulator that controls manganese homeostasis in Mycobacterium tuberculosis
Pandey, Molecular microbiology 2015 - “...TUBERCULIST ( http://genolist.pasteur.fr/tuberculist ). Rv no. Gene mRNA Wt LMn/HMn Function Rv0023 3.21.0 Transcriptional regulator Rv0105c rpmB 2.90.9 Ribosomal protein Rv0106 9.21.6 CMP Rv0280 54.229 PPE Rv0281 5.40.5 CMP Rv0282 6.61.5 CHP Rv0283 8.01.2 CMP Rv0284 7.20.8 CMP Rv0285 6.50.8 PE Rv0286 5.50.7 PPE Rv0287 esxG...”
- Zinc regulates a switch between primary and alternative S18 ribosomal proteins in Mycobacterium tuberculosis
Prisic, Molecular microbiology 2015 - “...of Cys (motif) L28-1 / L28-2/ L28-3 rpmB1 / rpmB2 /rpmB3 Rv2975A / Rv2058c / Rv0105c 4 (2 CxxC) / 1 / 1 L33-1 / L33-2 rpmG1 / rpmG2 Rv0634B / Rv2057c 4 (2 CxxC) / 0 S14-1 / S14-2 rpsN1 / rpsN2 Rv0717 / Rv2056c...”
- Physiology of mycobacteria
Cook, Advances in microbial physiology 2009 - “...S14 No 101 36 Rv0055 rpsR1 S18 84 54 Rv2055c rpsR2 S18 No 88 54 Rv0105c rpmB1 L28 No 94 53 Rv2058c rpmB2 L28 No 78 53 Rv2057c rpmG1 L33 No 54 30 Rv0634B rpmG2 L33 55 30 Table 6 Changes in the expression ratios of...”
- Global analysis of the Mycobacterium tuberculosis Zur (FurB) regulon
Maciag, Journal of bacteriology 2007 - “...5 RACE PCR of Rv2059 5 RACE PCR of Rv0105c 5 RACE PCR of Rv0105c proteins belonging to the ESAT-6/culture filtrate protein 10 (CFP-10) family. Characterization...”
- “...2. Genes under Zur transcriptional controla Locusb Gene Rv0105c rpmB1 q value (%)c Fold inductiond Gene product/function 2.7 Probable 50S ribosomal protein L28...”
- Conserved codon composition of ribosomal protein coding genes in Escherichia coli, Mycobacterium tuberculosis and Saccharomyces cerevisiae: lessons from supervised machine learning in functional genomics
Lin, Nucleic acids research 2002 - “...MT0733, MT0730, MT0741.1, MT2517, MT3052.2, MT2118, MT0114, MT0736, MT0728, MT0747, MT1337, MT2117.1, MT0663, MT4041.1, MT1680, MT3567.1, MT0729, MT0742,...”
RM24_NEUCR / Q7SC44 Large ribosomal subunit protein bL28m from Neurospora crassa (strain ATCC 24698 / 74-OR23-1A / CBS 708.71 / DSM 1257 / FGSC 987) (see 2 papers)
52% identity, 18% coverage
- function: Component of the mitochondrial ribosome (mitoribosome), a dedicated translation machinery responsible for the synthesis of mitochondrial genome-encoded proteins, including at least some of the essential transmembrane subunits of the mitochondrial respiratory chain. The mitoribosomes are attached to the mitochondrial inner membrane and translation products are cotranslationally integrated into the membrane.
subunit: Component of the mitochondrial large ribosomal subunit (mt- LSU). Mature N.crassa 74S mitochondrial ribosomes consist of a small (37S) and a large (54S) subunit. The 37S small subunit contains a 16S ribosomal RNA (16S mt-rRNA) and 32 different proteins. The 54S large subunit contains a 23S rRNA (23S mt-rRNA) and 42 different proteins.
6yweS structure of the mitoribosome from Neurospora crassa in the P/E tRNA bound state (see paper)
52% identity, 27% coverage
- Ligands: rna; magnesium ion (6yweS)
8fmwAZ / O51325 8fmwAZ (see paper)
34% identity, 76% coverage
AMUC_RS06345 50S ribosomal protein L28 from Akkermansia muciniphila
33% identity, 72% coverage
- The effect of bile acids on the growth and global gene expression profiles in Akkermansia muciniphila
Hagi, Applied microbiology and biotechnology 2020 - “...gene1223 Potassium-transporting ATPase subunit B WP_012420192.1 AMUC_RS02660 1.006 2.49E23 gene530 50S ribosomal protein L21 WP_012419537.1 AMUC_RS06345 0.957 7.49E26 gene1263 50S ribosomal protein L28 WP_012420229.1 AMUC_RS08450 0.948 4.78E22 gene1682 Nucleoside-diphosphate kinase WP_012420615.1 AMUC_RS09030 0.941 3.91E22 gene1798 Hypothetical protein WP_042448236.1 AMUC_RS11295 0.932 2.99E51 gene2253 Threonine dehydrogenase WP_012421139.1 AMUC_RS06355...”
Q72CS2 Large ribosomal subunit protein bL28 from Nitratidesulfovibrio vulgaris (strain ATCC 29579 / DSM 644 / CCUG 34227 / NCIMB 8303 / VKM B-1760 / Hildenborough)
52% identity, 54% coverage
- Synergy of Sodium Nitroprusside and Nitrate in Inhibiting the Activity of Sulfate Reducing Bacteria in Oil-Containing Bioreactors.
Fida, Frontiers in microbiology 2018 - “...2004 ). Proteins that showed decreased expression included ribosomal proteins (Q72CH7, Q72DH2, Q72CF7, Q728R7, Q728R8, Q72CS2, Q72DQ5, and Q72CF6), periplasmic-binding amino acid transporters (Q72E67, Q72F28, Q72F29, Q72EN0, Q72FN6, Q729Q3, and Q72CP5), tryptophan synthase (Q72EU7, Q72EU8, and Q72FX8), anthranilate synthase (Q72EV0, Q72EV1, Q72EV2, and Q72EV3), and antibiotic...”
GALLO_RS01760 50S ribosomal protein L28 from Streptococcus gallolyticus UCN34
59% identity, 44% coverage
- Genome-Based Drug Target Identification in Human Pathogen Streptococcus gallolyticus
Qureshi, Frontiers in genetics 2021 - “...RS01250 DEG10180105 47.283 AraC family transcriptional regulator GALLO_RS01215 DEG10110082 45.455 DNA polymerase III subunit alpha GALLO_RS01760 DEG10060346 44 50S ribosomal protein L28 GALLO_RS01960 DEG10470004 41.793 2-isopropylmalate synthase GALLO_RS02145 DEG10080178 40.355 Ribosome-binding factor A GALLO_RS02350 DEG10050423 39.623 Amino acid ABC transporter substrate-binding protein, PAAT family/amino acid ABC...”
5mrcS / P36525 of the yeast mitochondrial ribosome - Class A (see paper)
35% identity, 32% coverage
STACADC2_1717, STER_RS09470 50S ribosomal protein L28 from Streptococcus thermophilus
59% identity, 44% coverage
- Cell Proteins Obtained by Peptic Shaving of Two Phenotypically Different Strains of Streptococcus thermophilus as a Source of Anti-Inflammatory Peptides
Allouche, Nutrients 2022 - “...Cyto 8 29.50 STER_0568|ID:1899173|rplL| STER_RS02800 50S ribosomal subunit protein L7/L12 12.35 Cyto 21 61.79 STER_1936|ID:1899661| STER_RS09470 50S ribosomal protein L28 6.91 Cyto 18 96.83 8 61.91 STER_1899|ID:1900562|rpmC| STER_RS09305 50S ribosomal subunit protein L29 7.90 Cyto 12 68.12 STER_1889|ID:1900552|rpmD| STER_RS09255 50S ribosomal subunit protein L30 6.39 Cyto...”
- The complete genome sequence of the yogurt isolate Streptococcus thermophilus ACA-DC 2
Alexandraki, Standards in genomic sciences 2017 - “...as well as several ribosome binding proteins, were also identified (STACADC2_0137, STACADC2_1568-1569, STACADC2_1667, STACADC2_1669-1671, STACADC2_1675-1695, STACADC2_1717, STACADC2_1732-1733, STACADC2_1752, STACADC2_1755). Fig. 6 Additional genomic features of S. thermophilus ACA-DC 2. a Circular map of the S. thermophilus ACA-DC 2 genome as generated by IslandViewer 3. Highlighted regions...”
SPy1888 50S ribosomal protein L28 from Streptococcus pyogenes M1 GAS
45% identity, 60% coverage
spr0398 50S Ribosomal protein L28 from Streptococcus pneumoniae R6
SP_0441 50S ribosomal protein L28 from Streptococcus pneumoniae TIGR4
SM12261_RS08265 50S ribosomal protein L28 from Streptococcus mitis NCTC 12261
56% identity, 44% coverage
For advice on how to use these tools together, see
Interactive tools for functional annotation of bacterial genomes.
The PaperBLAST database links 793,807 different protein sequences to 1,259,118 scientific articles. Searches against EuropePMC were last performed on March 13 2025.
PaperBLAST builds a database of protein sequences that are linked
to scientific articles. These links come from automated text searches
against the articles in EuropePMC
and from manually-curated information from GeneRIF, UniProtKB/Swiss-Prot,
BRENDA,
CAZy (as made available by dbCAN),
BioLiP,
CharProtDB,
MetaCyc,
EcoCyc,
TCDB,
REBASE,
the Fitness Browser,
and a subset of the European Nucleotide Archive with the /experiment tag.
Given this database and a protein sequence query,
PaperBLAST uses protein-protein BLAST
to find similar sequences with E < 0.001.
To build the database, we query EuropePMC with locus tags, with RefSeq protein
identifiers, and with UniProt
accessions. We obtain the locus tags from RefSeq or from MicrobesOnline. We use
queries of the form "locus_tag AND genus_name" to try to ensure that
the paper is actually discussing that gene. Because EuropePMC indexes
most recent biomedical papers, even if they are not open access, some
of the links may be to papers that you cannot read or that our
computers cannot read. We query each of these identifiers that
appears in the open access part of EuropePMC, as well as every locus
tag that appears in the 500 most-referenced genomes, so that a gene
may appear in the PaperBLAST results even though none of the papers
that mention it are open access. We also incorporate text-mined links
from EuropePMC that link open access articles to UniProt or RefSeq
identifiers. (This yields some additional links because EuropePMC
uses different heuristics for their text mining than we do.)
For every article that mentions a locus tag, a RefSeq protein
identifier, or a UniProt accession, we try to select one or two
snippets of text that refer to the protein. If we cannot get access to
the full text, we try to select a snippet from the abstract, but
unfortunately, unique identifiers such as locus tags are rarely
provided in abstracts.
PaperBLAST also incorporates manually-curated protein functions:
- Proteins from NCBI's RefSeq are included if a
GeneRIF
entry links the gene to an article in
PubMed®.
GeneRIF also provides a short summary of the article's claim about the
protein, which is shown instead of a snippet.
- Proteins from Swiss-Prot (the curated part of UniProt)
are included if the curators
identified experimental evidence for the protein's function (evidence
code ECO:0000269). For these proteins, the fields of the Swiss-Prot entry that
describe the protein's function are shown (with bold headings).
- Proteins from BRENDA,
a curated database of enzymes, are included if they are linked to a paper in PubMed
and their full sequence is known.
- Every protein from the non-redundant subset of
BioLiP,
a database
of ligand-binding sites and catalytic residues in protein structures, is included. Since BioLiP itself
does not include descriptions of the proteins, those are taken from the
Protein Data Bank.
Descriptions from PDB rely on the original submitter of the
structure and cannot be updated by others, so they may be less reliable.
(For SitesBLAST and Sites on a Tree, we use a larger subset of BioLiP so that every
ligand is represented among a group of structures with similar sequences, but for
PaperBLAST, we use the non-redundant set provided by BioLiP.)
- Every protein from EcoCyc, a curated
database of the proteins in Escherichia coli K-12, is included, regardless
of whether they are characterized or not.
- Proteins from the MetaCyc metabolic pathway database
are included if they are linked to a paper in PubMed and their full sequence is known.
- Proteins from the Transport Classification Database (TCDB)
are included if they have known substrate(s), have reference(s),
and are not described as uncharacterized or putative.
(Some of the references are not visible on the PaperBLAST web site.)
- Every protein from CharProtDB,
a database of experimentally characterized protein annotations, is included.
- Proteins from the CAZy database of carbohydrate-active enzymes
are included if they are associated with an Enzyme Classification number.
Even though CAZy does not provide links from individual protein sequences to papers,
these should all be experimentally-characterized proteins.
- Proteins from the REBASE database
of restriction enzymes are included if they have known specificity.
- Every protein with an evidence-based reannotation (based on mutant phenotypes)
in the Fitness Browser is included.
- Sequence-specific transcription factors (including sigma factors and DNA-binding response regulators)
with experimentally-determined DNA binding sites from the
PRODORIC database of gene regulation in prokaryotes.
- Putative transcription factors from RegPrecise
that have manually-curated predictions for their binding sites. These predictions are based on
conserved putative regulatory sites across genomes that contain similar transcription factors,
so PaperBLAST clusters the TFs at 70% identity and retains just one member of each cluster.
- Coding sequence (CDS) features from the
European Nucleotide Archive (ENA)
are included if the /experiment tag is set (implying that there is experimental evidence for the annotation),
the nucleotide entry links to paper(s) in PubMed,
and the nucleotide entry is from the STD data class
(implying that these are targeted annotated sequences, not from shotgun sequencing).
Also, to filter out genes whose transcription or translation was detected, but whose function
was not studied, nucleotide entries or papers with more than 25 such proteins are excluded.
Descriptions from ENA rely on the original submitter of the
sequence and cannot be updated by others, so they may be less reliable.
Except for GeneRIF and ENA,
the curated entries include a short curated
description of the protein's function.
For entries from BioLiP, the protein's function may not be known beyond binding to the ligand.
Many of these entries also link to articles in PubMed.
For more information see the
PaperBLAST paper (mSystems 2017)
or the code.
You can download PaperBLAST's database here.
Changes to PaperBLAST since the paper was written:
- November 2023: incorporated PRODORIC and RegPrecise. Many PRODORIC entries were not linked to a protein sequence (no UniProt identifier), so we added this information.
- February 2023: BioLiP changed their download format. PaperBLAST now includes their non-redundant subset. SitesBLAST and Sites on a Tree use a larger non-redundant subset that ensures that every ligand is represented within each cluster. This should ensure that every binding site is represented.
- June 2022: incorporated some coding sequences from ENA with the /experiment tag.
- March 2022: incorporated BioLiP.
- April 2020: incorporated TCDB.
- April 2019: EuropePMC now returns table entries in their search results. This has expanded PaperBLAST's database, but most of the new entries are of low relevance, and the resulting snippets are often just lists of locus tags with annotations.
- February 2018: the alignment page reports the conservation of the hit's functional sites (if available from from Swiss-Prot or UniProt)
- January 2018: incorporated BRENDA.
- December 2017: incorporated MetaCyc, CharProtDB, CAZy, REBASE, and the reannotations from the Fitness Browser.
- September 2017: EuropePMC no longer returns some table entries in their search results. This has shrunk PaperBLAST's database, but has also reduced the number of low-relevance hits.
Many of these changes are described in Interactive tools for functional annotation of bacterial genomes.
PaperBLAST cannot provide snippets for many of the papers that are
published in non-open-access journals. This limitation applies even if
the paper is marked as "free" on the publisher's web site and is
available in PubmedCentral or EuropePMC. If a journal that you publish
in is marked as "secret," please consider publishing elsewhere.
Many important articles are missing from PaperBLAST, either because
the article's full text is not in EuropePMC (as for many older
articles), or because the paper does not mention a protein identifier such as a locus tag, or because of PaperBLAST's heuristics. If you notice an
article that characterizes a protein's function but is missing from
PaperBLAST, please notify the curators at UniProt
or add an entry to GeneRIF.
Entries in either of these databases will eventually be incorporated
into PaperBLAST. Note that to add an entry to UniProt, you will need
to find the UniProt identifier for the protein. If the protein is not
already in UniProt, you can ask them to create an entry. To add an
entry to GeneRIF, you will need an NCBI Gene identifier, but
unfortunately many prokaryotic proteins in RefSeq do not have
corresponding Gene identifers.
References
PaperBLAST: Text-mining papers for information about homologs.
M. N. Price and A. P. Arkin (2017). mSystems, 10.1128/mSystems.00039-17.
Europe PMC in 2017.
M. Levchenko et al (2017). Nucleic Acids Research, 10.1093/nar/gkx1005.
Gene indexing: characterization and analysis of NLM's GeneRIFs.
J. A. Mitchell et al (2003). AMIA Annu Symp Proc 2003:460-464.
UniProt: the universal protein knowledgebase.
The UniProt Consortium (2016). Nucleic Acids Research, 10.1093/nar/gkw1099.
BRENDA in 2017: new perspectives and new tools in BRENDA.
S. Placzek et al (2017). Nucleic Acids Research, 10.1093/nar/gkw952.
The EcoCyc database: reflecting new knowledge about Escherichia coli K-12.
I. M. Keeseler et al (2016). Nucleic Acids Research, 10.1093/nar/gkw1003.
The MetaCyc database of metabolic pathways and enzymes.
R. Caspi et al (2018). Nucleic Acids Research, 10.1093/nar/gkx935.
CharProtDB: a database of experimentally characterized protein annotations.
R. Madupu et al (2012). Nucleic Acids Research, 10.1093/nar/gkr1133.
The carbohydrate-active enzymes database (CAZy) in 2013.
V. Lombard et al (2014). Nucleic Acids Research, 10.1093/nar/gkt1178.
The Transporter Classification Database (TCDB): recent advances
M. H. Saier, Jr. et al (2016). Nucleic Acids Research, 10.1093/nar/gkv1103.
REBASE - a database for DNA restriction and modification: enzymes, genes and genomes.
R. J. Roberts et al (2015). Nucleic Acids Research, 10.1093/nar/gku1046.
Deep annotation of protein function across diverse bacteria from mutant phenotypes.
M. N. Price et al (2016). bioRxiv, 10.1101/072470.
by Morgan Price,
Arkin group
Lawrence Berkeley National Laboratory