PaperBLAST
PaperBLAST Hits for EX31_RS25170 (46 a.a., MKRTFQPSVL...)
Show query sequence
>EX31_RS25170
MKRTFQPSVLKRNRSHGFRARMATKNGRQVLARRRAKGRTRLSASK
Running BLASTp...
Found 70 similar proteins in the literature:
HSM_2021 50S ribosomal protein L34 from Haemophilus somnus 2336
93% identity, 96% coverage
Asuc_2117 ribosomal protein L34 from Actinobacillus succinogenes 130Z
HI0998 ribosomal protein L34 (rpL34) from Haemophilus influenzae Rd KW20
91% identity, 96% coverage
- Transcriptome analysis and anaerobic C4 -dicarboxylate transport in Actinobacillus succinogenes
Rhie, MicrobiologyOpen 2018 - “...Table S5 ). Genes encoding ribosomal proteins (Asuc_0015, Asuc_00445, Asuc_0520, Asuc_0525, Asuc_0721, Asuc_0774, Asuc_14934, and Asuc_2117) and their accessory proteins were among those classified into this cluster. In addition, members of the betaglucoside operon (Asuc_09725) and 11 genes related to the maltose operon (Asuc_03123, Asuc_03150323) were...”
- Initial proteome analysis of model microorganism Haemophilus influenzae strain Rd KW20
Kolker, Journal of bacteriology 2003 - “...HI0779 HI0789 HI1630 HI0879 HI0951 HI0785 HI0796 HI0758 HI0158 HI0950 HI0998 HI1319m HI0798.1 550 252 236 207 167 131 157 131 131 119 130 125 123 102 90 83...”
BU013 50S ribosomal protein L34 from Buchnera aphidicola str. APS (Acyrthosiphon pisum)
82% identity, 96% coverage
Bfl015 50s ribosomal protein l34 from Candidatus Blochmannia floridanus
78% identity, 98% coverage
8rd8Ba / A0A0M4TEZ6 8rd8Ba (see paper)
84% identity, 96% coverage
8cd14 / P29436 8cd14 (see paper)
PA5570 50S ribosomal protein L34 from Pseudomonas aeruginosa PAO1
IAU57_33160 50S ribosomal protein L34 from Pseudomonas aeruginosa
84% identity, 96% coverage
- Ligand: rna (8cd14)
- 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 - “...PA5276 PA5316 PA5355 PA5460 PA5490 PA5491 PA5555 PA5557 PA5569 PA5570 ispB glyA3 PA4608 PA4610 PA4633 PA4671 PA4692 PA4702 PA4739 pnp rbfA accB accC PA4880 rpsF...”
- Transcriptome analysis reveals that multidrug efflux genes are upregulated to protect Pseudomonas aeruginosa from pentachlorophenol stress
Muller, Applied and environmental microbiology 2007 - “...(cysD) PA4563 (rpsT) PA4748 (tpiA) PA4847 (accB) PA5013 (ilvE) PA5570 (rpmH) 13 h c VOL. 73, 2007 4557 vealed through the analysis of genome-wide expression...”
- Effect of anaerobiosis and nitrate on gene expression in Pseudomonas aeruginosa
Filiatrault, Infection and immunity 2005 - “...PA5496 PA5497 PA5504 PA5506 PA5507 PA5508 PA5510 PA5570 Gene 3768 INFECT. IMMUN. NOTES TABLE 2. Differentially expressed transcripts between cultures grown...”
- Complete Genome Sequence of Pseudomonas aeruginosa CMC-097, Isolated from a Ventilator-Associated Pneumonia Patient, Containing a Novel Carbapenem Resistance Class 1 Integron
Rao, Microbiology resource announcements 2021 - “...Genome Annotation Pipeline (PGAP) v5.0 ( 6 , 7 ) identified 6,632 genes (IAU57_00005 to IAU57_33160), including 6,467 protein-coding genes, 82 RNA genes (65 tRNAs, 12 rRNAs, and 5 noncoding RNAs), 83 pseudogenes, and 1 CRISPR array. BLAST analysis of the resulting genome found that it...”
B195_022465, FXO12_18260 50S ribosomal protein L34 from Pseudomonas sp. J380
81% identity, 93% coverage
- Role of DEAD-box RNA helicases in low-temperature adapted growth of Antarctic Pseudomonas syringae Lz4W
Hussain, Microbiology spectrum 2024 - “...at the National Center for Biotechnology Information site starts with locus tag number B195_000005 to B195_022465. For clarity on the figure, the common prefix B195_ has been omitted in the diagram. The direction of transcription is shown by arrows on above or below the gene-ORF boxes....”
- A Novel Marine Pathogen Isolated from Wild Cunners (Tautogolabrus adspersus): Comparative Genomics and Transcriptome Profiling of Pseudomonas sp. Strain J380
Umasuthan, Microorganisms 2021 - “...FXO12_13410, rplM ; FXO12_22175, rplF ; FXO12_24545, rplS ; FXO12_14665, rplY ; FXO12_26170, rpmF ; FXO12_18260, rpmH ; FXO12_11415, rpsB ; FXO12_15685, rpsF ; FXO12_22170, rpsH ; FXO12_13405, rpsI ; FXO12_14490, rpsT ; and FXO12_21760, rpsU ), elements or regulators involved in transcription (FXO12_23400, greA ;...”
- “...L32 RpmF 3.48 0 FXO12_13410 complement (2970861..2971289) rplM 50S ribosomal protein L13 RplM 3.04 0 FXO12_18260 4056006..4056140 rpmH 50S ribosomal protein L34 RpmH 2.79 7.9 10 15 FXO12_21760 Complement (4790073..4790288) rpsU 30S ribosomal protein S21 RpsU 3.24 0 FXO12_14490 3182295..3182573 rpsT 30S ribosomal protein S20 RpsT...”
PP0009 ribosomal protein L34 from Pseudomonas putida KT2440
81% identity, 93% coverage
A1S_2984 50S ribosomal protein L34 from Acinetobacter baumannii ATCC 17978
82% identity, 71% coverage
7m4v1 / B7IBH8 A. Baumannii ribosome-eravacycline complex: 50s (see paper)
ACIAD3684 50S ribosomal protein L34 from Acinetobacter sp. ADP1
82% identity, 96% coverage
VDA_003244 50S ribosomal protein L34 from Photobacterium damselae subsp. damselae CIP 102761
83% identity, 91% coverage
VC0007 ribosomal protein L34 from Vibrio cholerae O1 biovar eltor str. N16961
83% identity, 91% coverage
- Mining regulatory 5'UTRs from cDNA deep sequencing datasets
Livny, Nucleic acids research 2010 - “...Threonyl-tRNA synthetase T-box(60) RLE020 (5) C1 * 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...”
SsaF / b3703 50S ribosomal subunit protein L34 from Escherichia coli K-12 substr. MG1655 (see 31 papers)
rpmH / P0A7P5 50S ribosomal subunit protein L34 from Escherichia coli (strain K12) (see 30 papers)
RL34_ECOLI / P0A7P5 Large ribosomal subunit protein bL34; 50S ribosomal protein L34 from Escherichia coli (strain K12) (see 8 papers)
8a3l1 / P0A7P5 8a3l1 (see paper)
ECs4638 50S ribosomal subunit protein L34 from Escherichia coli O157:H7 str. Sakai
A6TG05 Large ribosomal subunit protein bL34 from Klebsiella pneumoniae subsp. pneumoniae (strain ATCC 700721 / MGH 78578)
B5QUQ1 Large ribosomal subunit protein bL34 from Salmonella enteritidis PT4 (strain P125109)
NP_418158 50S ribosomal subunit protein L34 from Escherichia coli str. K-12 substr. MG1655
P0A7P8 Large ribosomal subunit protein bL34 from Salmonella typhimurium (strain LT2 / SGSC1412 / ATCC 700720)
b3703 50S ribosomal protein L34 from Escherichia coli str. K-12 substr. MG1655
NP_709497 50S ribosomal subunit protein L34 from Shigella flexneri 2a str. 301
SPC_3926 50S ribosomal protein L34 from Salmonella enterica subsp. enterica serovar Paratyphi C strain RKS4594
SEN3656 50s ribosomal protein l34 from Salmonella enterica subsp. enterica serovar Enteritidis str. P125109
Z5194 50S ribosomal subunit protein L34 from Escherichia coli O157:H7 EDL933
93% identity, 100% coverage
- subunit: Part of the 50S ribosomal subunit.
- Ligand: rna (8a3l1)
- Global transcriptional response of Escherichia coli O157:H7 to growth transitions in glucose minimal medium
Bergholz, BMC microbiology 2007 - “...escC -2.00 1 ECs3559 srlA_1 2.08 3 ECs4632 yidA -2.02 1 ECs3595 rpoS 2.80 2 ECs4638 rpmH -2.47 1 ECs3606 cysD -2.59 1 ECs4639 rnpA -2.92 1 ECs3640 pyrG -2.98 1 ECs4679 atpE -2.33 1 ECs3659 fucO 2.17 3 ECs4716 rho -2.56 5 ECs3675 argA -4.09...”
- Disruption of KPC-producing Klebsiella pneumoniae membrane via induction of oxidative stress by cinnamon bark (Cinnamomum verum J. Presl) essential oil
Yang, PloS one 2019 - “...57 4-hydroxy-3-methylbut-2-enyl diphosphate reductase ispH A6T4G3 Isoprenoid biosynthesis Control 58 50S ribosomal protein L34 rpmH A6TG05 Protein biosynthesis Control 59 6-phosphogluconolactonase pgl A6T6J6 Carbohydrate metabolism Control 60 Adenine phosphoribosyltransferase apt A6T5N2 Purine metabolism Control 61 Aminomethyltransferase gcvT A6TDR7 Protein biosynthesis Control 62 Argininosuccinate synthase argG A6TEJ0...”
- Ethanol Adaptation Strategies in Salmonella enterica Serovar Enteritidis Revealed by Global Proteomic and Mutagenic Analyses
He, Applied and environmental microbiology 2019 (secret) - The sequence determination of a protein in a micro scale: the sequence analysis of ribosomal protein L34 of Escherichia coli.
Chen, Hoppe-Seyler's Zeitschrift fur physiologische Chemie 1976 (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 S13 rpsM 0.39 2.95E06 P0A7X3 Ribosomal subunit protein S9 rpsI 0.52 1.97E04 P0A7P5 Ribosomal subunit protein L34 rpmH 0.02 2.96E04 P0AG48 Ribosomal subunit protein L21 rplU 0.24 2.29E08 P0A7M9 Ribosomal subunit protein L31 rpmE 0.25 1.87E07 P62399 Ribosomal subunit protein L5 rplE 0.25...”
- Toward Single Bacterium Proteomics
Végvári, Journal of the American Society for Mass Spectrometry 2023 - “...more than half of the detected proteins, and importantly, one significantly enriched protein was ribosomal (P0A7P5, 50S ribosomal protein L34). Therefore, we decided that the freeze-and-thaw approach is suitable for single bacterium proteomics (SBP) analysis. Figure 1 Comparison of sample preparation methods in bulk proteomics. The...”
- N-dodecanoyl-homoserine lactone influences the levels of thiol and proteins related to oxidation-reduction process in Salmonella
de, PloS one 2018 - “...Translation ND ND 8.313 2.037 ND ND 7.849 1.076 ND ND 50S ribosomal protein L34 P0A7P8 rpmH Translation -7.903 2.324 ND ND ND ND 9.446 1.053 ND ND 30S ribosomal protein S1 Q7CQT9 rpsA Translation -3.033 4.181 ND ND 1.901 1.525 -1.215 0.505 ND ND 30S...”
- Depletion of the non-coding regulatory 6S RNA in E. coli causes a surprising reduction in the expression of the translation machinery
Neusser, BMC genomics 2010 - “...rpoB 0.53 DNA-directed RNA polymerase subunit beta (L10 operon) b3555 yiaG 0.52 predicted transcriptional regulator b3703 rpmH 0.45 50S ribosomal protein L34 b1235 rssB 0.11 response regulator of RpoS 1 Meaningful genes were selected by the following criteria: known or predicted function related to the ssrS...”
- Remaining flexible in old alliances: functional plasticity in constrained mutualisms
Wernegreen, DNA and cell biology 2009 - “...b1716 Bpen365 Bfl354 WGLp084 BU128 BUsg120 Bbp122 rpmH b3703 Bpen014 Bfl015 WGLp014 BU013 BUsg013 Bbp013 rpoD b3067 Bpen057 Bfl056 WGLp468 BU055 BUsg052 Bbp052...”
- Global gene expression profiling of asymptomatic bacteriuria Escherichia coli during biofilm growth in human urine
Hancock, Infection and immunity 2007 - “...rpmH bfr yhhW pdhR rplK iscR rseA yceD ryhB Z5401 b0990 b3703 b3336 c4228 b0113 b3983 b2531 b2572 b1088 b4451 Z5401 5S rRNA 23S rRNA 16S rRNA 10Sa RNA (tmRNA);...”
- Analysis of promoter targets for Escherichia coli transcription elongation factor GreA in vivo and in vitro
Stepanova, Journal of bacteriology 2007 - “...protein L33 50S ribosomal subunit protein L28 rpmH rnpA b3703 b3704 2.4 2.6 50S ribosomal subunit protein L34 RNase P, protein component; protein C5 atpD atpG...”
- Microarray analysis of orthologous genes: conservation of the translational machinery across species at the sequence and expression level
Jiménez, Genome biology 2003 - “...Orotate phosphoribosyltransferase Ribonuclease and pyrimidine biosynthesis b3643 Yes** COG0689 J Ribonuclease PH Ribosomal protein 14 b3703 Yes COG0230 J4 Ribosomal protein L34 Ribosomal protein 14 b3704 No COG0594 J Ribonuclease P protein component Protein export and transcription b3981 No COG0690 N Preprotein translocase secE subunit Protein...”
- 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 - “...yjjT zwf b3318 b3309 b2185 b3185 b3637 b3302 b3636 b3703 b3299 b3295 b3314 b3296 b3303 b4200 b3341 b3306 b3230 b3321 b3297 b3298 b3307 b2609 b3311 b4202 b3316...”
- 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 L31 Cytoplasm No Hits 18 NP_707005 50S ribosomal protein L32 Cytoplasm No Hits 19 NP_709497 50S ribosomal protein L34 Cytoplasm No Hits 20 NP_707397 50S ribosomal protein L35 Cytoplasm No Hits 21 NP_709083 DNA-directed RNA polymerase subunit alpha Cytoplasm No Hits 22 NP_706830 30S ribosomal...”
- Antibacterial Components and Modes of the Methanol-Phase Extract from Commelina communis Linn
Liu, Plants (Basel, Switzerland) 2023 - “...ribosomal protein L13 SPC_3414 0.179 30S ribosomal protein S9 SPC_3503 0.233 30S ribosomal protein S3 SPC_3926 0.238 50S ribosomal protein L34 SPC_3285 0.263 30S ribosomal protein S21 SPC_3372 0.306 50S ribosomal protein L27 SPC_3373 0.326 50S ribosomal protein L21 SPC_3502 0.336 50S ribosomal protein L16 SPC_4538...”
- Global transcriptomic analysis of ethanol tolerance response in Salmonella Enteritidis
He, Current research in food science 2022 - “...S2 SEN3242 rplQ 4.30 50S ribosomal protein L17 SEN3262 rpsC 3.69 30S ribosomal protein S3 SEN3656 rpmH 3.17 50S ribosomal protein L34 SEN3265 rplB 3.80 50S ribosomal protein L2 SEN3256 rplE 3.10 50S ribosomal protein L5 SEN3936 rplL 3.73 50S ribosomal protein L7/L12 SEN1709 rpmI 2.99...”
- Transcriptional responses of Escherichia coli K-12 and O157:H7 associated with lettuce leaves
Fink, Applied and environmental microbiology 2012 - “...Z5556 Z4589 Z4680 Z4674 Z4689 Z4679 Z3444 Z5061 Z5060 Z5194 Z0180 Z4666 Z4673 Z5809 Z4676 Z4692 Z4667 Z4700 Z4668 Z4677 Z4526 Z3903 Z5811 Z0027 Z4418 Z2230...”
BB0440 ribosomal protein L34 (rpmH) from Borrelia burgdorferi B31
69% identity, 88% coverage
SMc04434 PROBABLE 50S RIBOSOMAL PROTEIN L34 from Sinorhizobium meliloti 1021
73% identity, 96% coverage
BF0487 50S ribosomal protein L34 from Bacteroides fragilis YCH46
71% identity, 85% coverage
RL34_DEIRA / Q9RSH2 Large ribosomal subunit protein bL34; 50S ribosomal protein L34 from Deinococcus radiodurans (strain ATCC 13939 / DSM 20539 / JCM 16871 / CCUG 27074 / LMG 4051 / NBRC 15346 / NCIMB 9279 / VKM B-1422 / R1) (see 6 papers)
7a0r2 / Q9RSH2 50s deinococcus radiodurans ribosome bounded with mycinamicin i (see paper)
67% identity, 96% coverage
- function: Binds the 23S rRNA
subunit: Part of the 50S ribosomal subunit. Contacts protein L4. - Ligand: rna (7a0r2)
FTH_0169 ribosomal protein L34 from Francisella tularensis subsp. holarctica OSU18
70% identity, 96% coverage
SUB1659A 50S ribosomal protein L34 from Streptococcus uberis 0140J
70% identity, 96% coverage
- Prediction of Streptococcus uberis clinical mastitis treatment success in dairy herds by means of mass spectrometry and machine-learning
Maciel-Guerra, Scientific reports 2021 - “...and SUB0788) while ten proteins had known functions: four of them were 50S ribosomal proteins (SUB1659A, SUB0086, SUB1795 and SUB0076) two of them were 30S ribosomal proteins (SUB0689 and SUB0956), and the four remaining proteins were bacteriocin (SUB0512), translation initiation factor (SUB0090), DNA-binding (SUB1267), and a...”
- “...proteins. Peak mass Protein (MW) Locus ID (Gene ID) Location 5377.47Da 50S ribosomal L34 (5377.39Da) SUB1659A ( rpmH ) Cytoplasmic 6386.04Da a 50S ribosomal L30 (6385.58Da) SUB0086 ( rpmD ) Cytoplasmic 6386.04Da a Hypothetical Protein (6381.39Da) SUB1598 ( SUB1598 ) Unknown 6386.04Da a Hypothetical Protein (6382.44Da)...”
PGN_0694 50S ribosomal protein L34 from Porphyromonas gingivalis ATCC 33277
PG0656 ribosomal protein L34 from Porphyromonas gingivalis W83
F452_RS0103440 50S ribosomal protein L34 from Porphyromonas gulae DSM 15663
69% identity, 90% coverage
- Synthesis of ppGpp impacts type IX secretion and biofilm matrix formation in Porphyromonas gingivalis
Kim, NPJ biofilms and microbiomes 2020 - “...PGN_0637 htrA Heat shock-related protease htrA protein 1.93 PGN_0639 rpsF 30S ribosomal protein S6 1.77 PGN_0694 rpmH 50S ribosomal protein L34 2.09 PGN_0963 infC Translation initiation factor IF-3 2.10 PGN_0965 rplT 50S ribosomal protein L20 2.08 PGN_1580 rpsU 30S ribosomal protein S21 2.04 PGN_1647 rpmA 50S...”
- Microarray analysis of the transcriptional responses of Porphyromonas gingivalis to polyphosphate
Moon, BMC microbiology 2014 - “...ribosomal protein L27 1.78 PG0385 Ribosomal protein S21 3.98 PG0592 50S ribosomal protein L31 4.01 PG0656 50S ribosomal protein L34 6.80 PG0989 50S ribosomal protein L20 3.43 PG0990 Ribosomal protein L35 1.74 PG1723 Ribosomal protein S20 2.94 PG1758 Ribosomal protein S15 6.23 PG1959 Ribosomal protein L33...”
- Role of the Porphyromonas gingivalis extracytoplasmic function sigma factor, SigH
Yanamandra, Molecular oral microbiology 2012 - “...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 also...”
- “...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 0.949020 1.930561 22.713565 0.000000 (1.4E-10) 12 PG1664 ABC transporter, permease protein, putative 0.942746 1.922183 24.905838 0.000000 (5.0E-11) 12 PG0607 Hypothetical protein 0.934248 1.910894 26.892089 0.000000 (2.2E-11) 12...”
- Tetratricopeptide repeat protein-associated proteins contribute to the virulence of Porphyromonas gingivalis
Kondo, Infection and immunity 2010 - “...protein Upregulated genes PG0327 PG0373 PG0546 PG0635 PG0656 PG0722 PG0969 PG1532 PG1866 PG2006 PG2225 Hypothetical protein Hypothetical protein Hypothetical...”
- Adaptation of Porphyromonas gingivalis to microaerophilic conditions involves increased consumption of formate and reduced utilization of lactate
Lewis, Microbiology (Reading, England) 2009 - “...growth Gene ID* MD Fldd P value Repeat PG0656 PG2046 PG0214 PG1518 PG0538 PG1340 PG1378 PG2040 PG1138 PG2061 PG2105 PG0539 21.167622 21.066924 20.955201...”
- Antibacterial effects of sodium tripolyphosphate against Porphyromonas species associated with periodontitis of companion animals
Lee, Journal of veterinary science 2019 - “...+10.28 F452_RS0100215 50S ribosomal protein L27 3.46E-33 +4.18 F452_RS0106830 30S ribosomal protein S15 1.30E-41 +6.20 F452_RS0103440 50S ribosomal protein L34 4.64E-96 +14.01 F452_RS0103375 50S ribosomal protein L20 1.97E-26 +3.66 * F452_RS0100210 50S ribosomal protein L21 4.76E-35 +3.65 * F452_RS0103380 50S ribosomal protein L35 9.81E-24 +3.60 *...”
RL34_BACSU / P05647 Large ribosomal subunit protein bL34; 50S ribosomal protein L34 from Bacillus subtilis (strain 168) (see paper)
Q65CM7 Large ribosomal subunit protein bL34 from Bacillus licheniformis (strain ATCC 14580 / DSM 13 / JCM 2505 / CCUG 7422 / NBRC 12200 / NCIMB 9375 / NCTC 10341 / NRRL NRS-1264 / Gibson 46)
BSU41060 50S ribosomal protein L34 from Bacillus subtilis subsp. subtilis str. 168
70% identity, 96% coverage
stu1808 50S ribosomal protein L34 from Streptococcus thermophilus LMG 18311
68% identity, 96% coverage
SM12261_RS01350 50S ribosomal protein L34 from Streptococcus mitis NCTC 12261
SPD_1790 ribosomal protein L34 from Streptococcus pneumoniae D39
70% identity, 96% coverage
LMRG_02427 ribosomal protein L34 from Listeria monocytogenes 10403S
Q71VQ6 Large ribosomal subunit protein bL34 from Listeria monocytogenes serotype 4b (strain F2365)
lmo2856 ribosomal protein L34 from Listeria monocytogenes EGD-e
70% identity, 96% coverage
- Listeria monocytogenes σA Is Sufficient to Survive Gallbladder Bile Exposure
Boonmee, Frontiers in microbiology 2019 - “...base plate protein gp18 [Bacteriophage A118] 2.1 0.04 LMRG_02423 lmo2852 ASCH domain-containing protein 2.02 0.02 LMRG_02427 lmo2856 rpmH 50S ribosomal protein L34 2.06 0.00 LMRG_02611 lmo0265 dapE Succinyl-diaminopimelate desuccinylase 2.87 0.00 LMRG_02646 lmo0263 inlC2 , inlH Internalin C2 2.22 0.04 LMRG_02700 lmo2568 LMRG_02700-LMRG_02701 Hypothetical protein 9.41...”
- 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 - “...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 155 Q71XL9 0.743 Non-allergen 156 Q720B5 0.934 Non-allergen 157 Q71XA1 1.344 Non-allergen 158 A6X137 0.435 Non-allergen 159 Q71Z99 0.409 Non-allergen...”
- “...RKSRSGNKR 40.5 2.7338 Antigen Q71WI2 DRB1_1301 LLTRDPRMK 16.6 1.3863 Antigen DRB1_1301 KSSVARVRL 68.6 1.0414 Antigen Q71VQ6 DRB1_1301 ASRRRKGRK 8.3 2.0002 Antigen DRB1_1301 SRRRKGRKV 12.1 1.7764 Antigen DRB1_1301 MSTKNGRRV 13.5 1.7661 Antigen DRB1_1301 FRTRMSTKN 39.7 1.2896 Antigen DRB1_1301 RMSTKNGRR 49.3 2.0073 Antigen Q722D6 DRB1_0101 YALLFFPYA 1222 1.9423...”
- Whole genome genetic variation and linkage disequilibrium in a diverse collection of Listeria monocytogenes isolates
Louha, PloS one 2021 - “...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 lmo1469 rpsU 454 20.34 1501881..1502054 core small subunit ribosomal protein S21...”
- “...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 theory [...”
- Listeria monocytogenes σA Is Sufficient to Survive Gallbladder Bile Exposure
Boonmee, Frontiers in microbiology 2019 - “...plate protein gp18 [Bacteriophage A118] 2.1 0.04 LMRG_02423 lmo2852 ASCH domain-containing protein 2.02 0.02 LMRG_02427 lmo2856 rpmH 50S ribosomal protein L34 2.06 0.00 LMRG_02611 lmo0265 dapE Succinyl-diaminopimelate desuccinylase 2.87 0.00 LMRG_02646 lmo0263 inlC2 , inlH Internalin C2 2.22 0.04 LMRG_02700 lmo2568 LMRG_02700-LMRG_02701 Hypothetical protein 9.41 0.00...”
- Transcriptional and phenotypic responses of Listeria monocytogenes to chlorine dioxide
Pleitner, Applied and environmental microbiology 2014 - “...lmo1658 lmo1755 lmo2047 lmo2597 lmo2633 lmo2811 lmo2856 Purines, pyrimidines, nucleosides, and nucleotides lmo1827 lmo1929 lmo0509 lmo1096 Annotationc Fold...”
- Microarray-based characterization of the Listeria monocytogenes cold regulon in log- and stationary-phase cells
Chan, Applied and environmental microbiology 2007 - “...including lmo1480, lmo1787, lmo2548, lmo2620, lmo2627, and lmo2856 (see Table S2 in the supplemental material). Operons encoding PTS-associated proteins (Fig....”
NE0390 Ribosomal protein L34 from Nitrosomonas europaea ATCC 19718
64% identity, 96% coverage
AT3G13882 structural constituent of ribosome from Arabidopsis thaliana
67% identity, 21% coverage
- Genome-wide association studies from spoken phenotypic descriptions: a proof of concept from maize field studies
Yanarella, G3 (Bethesda, Md.) 2024 - “...(222915976) 3-219281938 (222864957) 18 Total Zm00001d044242 bHLH-transcription factor25 (bhlh25) 5 unrelated AT3G21330 Zm00001d044255 6 unrelated AT3G13882 Zm00001d044260 12 unrelated AT5G56930 8-665419 (801635) c 8-872459 (1016749) 15 Total Zm00001d008200 proteolipid membrane potential regulator7 (pmpm7) GO:0009737 Response to abscisic acid + 4 unrelated Zm00001d008201 aux/iaa transcription factor34 (iaa34)...”
- “...in photoresponsiveness for hypocotyl length; Khanna et al . 2006 ), Zm00001d044255 ( Arabidopsis ortholog AT3G13882 is involved in plant growth rates and flowering; Xu et al . 2023 ), and Zm00001d044260, the gene c3h2 , with c3h genes showing some height-related phenotypic involvement ( Fornal...”
- Genome-wide association study of aphid abundance highlights a locus affecting plant growth and flowering in Arabidopsis thaliana
Xu, Royal Society open science 2023 - “...inflorescence. Out of candidate genes near this significant variant, a mutant of a ribosomal gene (AT3G13882) exhibited slower growth and later flowering than a wild type under laboratory conditions. A no-choice assay with the turnip aphid, Lipaphis erysimi , found that aphids were unable to successfully...”
- “...NASC Accession ID: N70000) wild type, we ordered four mutant lines for a ribosomal gene (AT3G13882) (electronic supplementary material, table S2). These original mutants were backcrossed with the Col-0 wild type three times. Following the instructions [ 37 ], we examined the insertion site by polymerase...”
- Genome-wide association study highlights escape from aphids by delayed growth inArabidopsis thaliana
Xu, 2022
TDE2400 ribosomal protein L34 from Treponema denticola ATCC 35405
71% identity, 88% coverage
- Transcriptional responses of Treponema denticola to other oral bacterial species
Sarkar, PloS one 2014 - “...hypothetical protein 2.83 TDE2398 conserved hypothetical protein 1.92 TDE2399 rnpA ribonuclease P protein component 2.36 TDE2400 ribosomal protein L34 1.50 TDE2410 Hemolysin 2.29 See legend Table 3 . Yellow complex species While there was considerable overlap between the transcriptional changes of T. denticola in the presence...”
C6B32_03095 50S ribosomal protein L34 from Campylobacter fetus subsp. testudinum
64% identity, 96% coverage
- Differentiation of Campylobacter fetus Subspecies by Proteotyping
Emele, European journal of microbiology & immunology 2019 - “...Locus Tag Protein ID L36 1 MK463617 L34 1 CP000487.1:557520557,654 CFF8240_0551 ABK82017.1 L34 2 CP027287.1:608973609,107 C6B32_03095 AVK80859.1 L32-M 1 CP000487.1:210702210,848 CFF8240_0235 ABK81894.1 L32-M 6 MK463615 L33-M 1 CP000487.1:13138471,313,949 CFF8240_1324 ABK82614.1 L33-M 3 CP027287.1:c13989131,398,746 C6B32_06940 AVK81560.1 L33-M 5 MK463616 S14-M 1 CP000487.1:3952639,711 CFF8240_0047 ABK82398.1 L29 1 CP000487.1:3792538,110...”
CFF8240_0551 ribosomal protein L34 from Campylobacter fetus subsp. fetus 82-40
64% identity, 96% coverage
- Differentiation of Campylobacter fetus Subspecies by Proteotyping
Emele, European journal of microbiology & immunology 2019 - “...Biomarker Isoform Gene Bank Accession Locus Tag Protein ID L36 1 MK463617 L34 1 CP000487.1:557520557,654 CFF8240_0551 ABK82017.1 L34 2 CP027287.1:608973609,107 C6B32_03095 AVK80859.1 L32-M 1 CP000487.1:210702210,848 CFF8240_0235 ABK81894.1 L32-M 6 MK463615 L33-M 1 CP000487.1:13138471,313,949 CFF8240_1324 ABK82614.1 L33-M 3 CP027287.1:c13989131,398,746 C6B32_06940 AVK81560.1 L33-M 5 MK463616 S14-M 1 CP000487.1:3952639,711...”
BPSL0075a 50S ribosomal protein L34 from Burkholderia pseudomallei K96243
BRPE64_RS14035 50S ribosomal protein L34 from Burkholderia pseudomallei MSHR146
65% identity, 93% coverage
- 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 - “...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 the WT (Fig. S5). Consequently, we compared...”
- Transposon sequencing reveals the essential gene set and genes enabling gut symbiosis in the insect symbiont Caballeronia insecticola
Jouan, ISME communications 2024 - “...principal chromosome of B. cenocepacia , carrying on the replication origin locus the genes rpmH (BRPE64_RS14035), rnpA (BRPE64_RS14030), dnaA (BRPE64_RS00005), dnaN (BRPE64_RS00010), and gyrB (BRPE64_RS00015), and on a nearby locus the chromosome partitioning genes parA (BRPE64_RS13400) and parB (BRPE64_RS13395) [ 34 , 35 ]. Except for...”
LOC103870086 uncharacterized protein LOC103870086 from Brassica rapa
67% identity, 29% coverage
FE46_RS03875 50S ribosomal protein L34 from Flavobacterium psychrophilum
68% identity, 83% coverage
5nrg2 / Q2FUQ0 The crystal structure of the large ribosomal subunit of staphylococcus aureus in complex with rb02 (see paper)
6dddP Structure of the 50s ribosomal subunit from methicillin resistant staphylococcus aureus in complex with the oxazolidinone antibiotic lzd-5 (see paper)
66% identity, 96% coverage
NGO2182 hypothetical protein from Neisseria gonorrhoeae FA 1090
66% identity, 96% coverage
- Deep sequencing-based analysis of the anaerobic stimulon in Neisseria gonorrhoeae
Isabella, BMC genomics 2011 - “...Nitrite reductase NsrR, FNR eftD NGO1396 5.2 5.1 Electron transfer flavoprotein-ubiquinone oxidoreductase Macromolecular biosynthesis rl34 NGO2182 3.0 3. 1 50S ribosomal protein L34 Regulation farR NGO0058 4.0 3.7 MarR family transcriptional regulator Lrp, MtrR nmlR NGO0602 7.2 7.6 Transcriptional regulator nmlR NmlR, FNR xre NGO0797 3.2...”
YSS_RS04330 50S ribosomal protein L34 from Campylobacter coli RM4661
CJJ81176_0984 ribosomal protein L34 from Campylobacter jejuni subsp. jejuni 81-176
64% identity, 96% coverage
- Proteotyping as alternate typing method to differentiate Campylobacter coli clades
Emele, Scientific reports 2019 - “...product Forward primer (53) Reverse primer (53) Amplicon length [bp] YSS_RS00895 RpmJ/L36 AGCTGCTGCTTCATCTTCACT AGCCTTGATAAAGGGCGTATC 490 YSS_RS04330 RpmH/L34 AAATGCTCGGGCAAATTGATTA GCCATCGCAATACCACTTTT 512 YSS_RS01420 RpmF/L32 TGCACCACTATGTCCTGCTG TGCCACAATGCAAGGTTTTGT 728 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...”
- Campylobacter jejuni Virulence Factors Identified by Modulating Their Synthesis on Ribosomes With Altered rRNA Methylation
Sałamaszyńska-Guz, Frontiers in cellular and infection microbiology 2021 - “...PseA CJJ81176_1333 Uncharacterized protein CJJ81176_1104 Anthranilate synthase component I, TrpE CJJ81176_0369 50S ribosomal protein L34 CJJ81176_0984 Basal-body rod modification protein, FlgD CJJ81176_0080 ATP synthase subunit c, AtpE CJJ81176_0943 Flagellar basal-body rod protein, FlgG CJJ81176_0721 Lipoprotein, putative CJJ81176_1640 Flagellin CJJ81176_1338 Acetyltransferase, GNAT CJJ81176_0250 N-(5-phosphoribosyl)anthranilate isomerase, TrpF CJJ81176_0371...”
SAS093 50S ribosomal protein L34 from Staphylococcus aureus subsp. aureus N315
SAOUHSC_03055 ribosomal protein L34 from Staphylococcus aureus subsp. aureus NCTC 8325
SERP0001 ribosomal protein L34 from Staphylococcus epidermidis RP62A
B4602_RS14385, EKM74_RS07590 50S ribosomal protein L34 from Staphylococcus aureus
66% identity, 96% coverage
- Transcriptional profiles of the response of methicillin-resistant Staphylococcus aureus to pentacyclic triterpenoids
Chung, PloS one 2013 - “...50S ribosomal protein L32 7.7 Translation SAS042 rpmG 50S ribosomal protein L33 1,2,3 8.4 Translation SAS093 rpmH 50S ribosomal protein L34 6.3 Translation SA1503 rpmI 50S ribosomal protein L35 6.0 Translation SAS078 rpmJ 50S ribosomal protein L36 21.0 Translation SA2035 rplE 50S ribosomal protein L5 6.3...”
- Transcription profiling-based identification of Staphylococcus aureus genes regulated by the agr and/or sarA loci
Dunman, Journal of bacteriology 2001 - “...SA1103 SA0523 SA0666 SA1391 SA1123 SA2351 SA0016 SA1045 SAS093 SA1466 SA1844 SA1842 SA1843 SAS066 SA1516 SA0434 SA1120 SA1920 SA2079 SA2135 SA1214 SA0099 SA0100...”
- Insights Into the Impact of Small RNA SprC on the Metabolism and Virulence of Staphylococcus aureus
Zhou, Frontiers in cellular and infection microbiology 2022 - “...SAOUHSC_02881 SA2351 -85.3 SAOUHSC_00871 dltc -66.1 SAOUHSC_01452 ald -84.9 SAOUHSC_03045 cspB -65.7 SAOUHSC_00788 SA0721 -84.4 SAOUHSC_03055 rpmH -61 SAOUHSC_01955 lukE -83.7 SAOUHSC_02853 SA2331 -59.8 SAOUHSC_01424 murG -83.6 SAOUHSC_01336 SA1176 -54.4 SAOUHSC_02329 thiM -82.9 All the mRNAs transcribed by DEGs with defined functions were predicted the ability...”
- Insights into the global effect on Staphylococcus aureus growth arrest by induction of the endoribonuclease MazF toxin
Sierra, Nucleic acids research 2020 - “...[145/UACACA] n/a SAOUHSC_02519 SAOUHSC_02519 Hypothetical protein [406/UACAUA] n/a SAOUHSC_02827 SAOUHSC_02827 Hypothetical protein [167/UACUUA] n/a rpmH SAOUHSC_03055 50S ribosomal protein L34 [12/UACUUA] Structural constituent of ribosome [GO:0003735] rpsF SAOUHSC_00348 30S ribosomal protein S6 [6/AACAUA] [22/UACAUC] Structural constituent of ribosome [GO:0003735] fusA SAOUHSC_00529 Elongation factor G 2/UACAUG[] [829/UACUUA]...”
- Low-level predation by lytic phage phiIPLA-RODI promotes biofilm formation and triggers the stringent response in Staphylococcus aureus
Fernández, Scientific reports 2017 - “...SAOUHSC_02969 arcA Arginine deiminase 5.89 SAOUHSC_03002 zwf Poly-beta-1,6-N-acetyl-D-glucosamine synthase 3.16 SAOUHSC_03002 icaA Poly-beta-1,6-N-acetyl-D-glucosamine synthase 3.16 SAOUHSC_03055 rpmH 50S ribosomal protein L34 3.07 Table 2 Confirmation by RT-qPCR of the dysregulation for selected genes identified by RNA-seq analysis. Gene Gene product FC (RT-qPCR) FC (RNA-seq) atl Bifunctional...”
- Deciphering the Antibacterial Mode of Action of Alpha-Mangostin on Staphylococcus epidermidis RP62A Through an Integrated Transcriptomic and Proteomic Approach
Sivaranjani, Frontiers in microbiology 2019 - “...mechanosensitive channel protein -1.53 1.31 10 -06 SERP0013 Conserved hypothetical protein -1.33 1.54 10 -06 SERP0001 rpmH Ribosomal protein L34 -2.37 1.95 10 -06 SERP2271 Conserved hypothetical protein -2.07 2.95 10 -06 SERP0557 Conserved hypothetical protein -1.39 3.64 10 -06 SERP1946 Transcriptional regulator, TetR family -1.65...”
- Staphylococcus epidermidis SrrAB regulates bacterial growth and biofilm formation differently under oxic and microaerobic conditions
Wu, Journal of bacteriology 2015 - “...Protein synthesis SERP0840 SERP0046 SERP1153 SERP1284 SERP1821 SERP0807 SERP0001 SERP2371 SERP2105 SERP2107 rpsO rpsR rpsT rpsD rplN rplS rpmH opp-1B pgsA pgsB...”
- Combined proteomic and transcriptomic analysis of the antimicrobial mechanism of tannic acid against Staphylococcus aureus
Wang, Frontiers in pharmacology 2023 - “...2.13 0.78 B4602_RS09915 - WP_000544969.1 Type 1 glutamine amidotransferase 0.16 0.34 Ribosome and protein synthesis B4602_RS14385 rpmH WP_000240855.1 50S ribosomal protein L34 0.49 3.24 B4602_RS11790 rplP WP_000926310.1 50S ribosomal protein L16 1.62 0.48 B4602_RS11810 rplB WP_000985472.1 50S ribosomal protein L2 1.86 0.96 B4602_RS11710 rpmJ WP_000868342.1 50S...”
- Transcriptomic Analysis Revealed Antimicrobial Mechanisms of Lactobacillus rhamnosus SCB0119 against Escherichia coli and Staphylococcus aureus
Peng, International journal of molecular sciences 2022 - “...ribosomal protein S10 EKM74_RS07510 151.39 9.3 705.28 120.89 2.219912 rplI ; 50S ribosomal protein L9 EKM74_RS07590 114.58 17.68 1144.54 138.16 3.320336 rpmH ; 50S ribosomal protein L34 EKM74_RS10450 236.72 37.3 7542.84 237.11 4.993827 rpsF ; 30S ribosomal protein S6 EKM74_RS10460 55.84 4.69 531.48 99.45 3.250636 rpsR...”
GRMZM2G126603 LIN1 protein from Zea mays
64% identity, 31% coverage
6o8w4 / A0A1B4XSI4 6o8w4 (see paper)
IUJ47_RS03805 50S ribosomal protein L34 from Enterococcus faecalis
EF3333 ribosomal protein L34 from Enterococcus faecalis V583
66% identity, 96% coverage
Q81JG9 Large ribosomal subunit protein bL34 from Bacillus anthracis
66% identity, 96% coverage
- Identification of Bacillus anthracis by using matrix-assisted laser desorption ionization-time of flight mass spectrometry and artificial neural networks
Lasch, Applied and environmental microbiology 2009 - “...2,708 2,813 2,944 3,068 3,080 3,132 3,214 3,247 Q81JG9 Q81Y79 Q81U79 Unassigned Q81LW9 Unassigned Unassigned Q6HUG3 Q81VR2 Unassigned 3,322 3,340 3,418 3,541...”
- “...Q81VA0 Q81KT1 Q81QJ2 Q6EZN2 Q81U02 Q81XK6 Unassigned Q81JG9 Unassigned Q81U86 Q81Y79 Q81U79 Q81LW9 Q81U56 Q6HUG3 Unassigned Q81VR2 Unassigned Q81LS7 Q81KU1...”
MHO_0030 50S ribosomal protein L34 from Mycoplasma hominis
64% identity, 94% coverage
9c4g1 / A0A2B7IDI8 Cutibacterium acnes 50s ribosomal subunit with clindamycin bound (see paper)
66% identity, 96% coverage
8p7x0 / P78006 8p7x0 (see paper)
MPN682 ribosomal protein L34 from Mycoplasma pneumoniae M129
62% identity, 94% coverage
- Ligand: rna (8p7x0)
- Evolution of mosaic operons by horizontal gene transfer and gene displacement in situ
Omelchenko, Genome biology 2003 - “...Actinobacteria Succinate dehydrogenase subunit C Cluster 29 Mycoplasma genitalium Mycoplasma pneumoniae MG461-466 MPN677-682 Housekeeping MG466 MPN682 Gram-negative bacteria Ribosomal protein L34 Cluster 34 Thermotoga maritima TM0548-0556 Leucine/isoleucine biosynthesis TM0552 TM0555 TM0554 2-Isopropylmalate synthase 3-Isopropylmalate dehydratase, small subunit 3-Isopropylmalate dehydratase, large subunit Pyrococcus abyssi PAB888-895 PAB0890 PAB0893...”
HL033_03600 50S ribosomal protein L34 from Neoehrlichia mikurensis
64% identity, 96% coverage
Kole_0258 50S ribosomal protein L34 from Kosmotoga olearia TBF 19.5.1
Kole_0258 ribosomal protein L34 from Thermotogales bacterium TBF 19.5.1
61% identity, 96% coverage
CD3680 50S ribosomal protein L34 from Clostridium difficile 630
64% identity, 91% coverage
- Genome-Wide Transcription Start Site Mapping and Promoter Assignments to a Sigma Factor in the Human Enteropathogen Clostridioides difficile
Soutourina, Frontiers in microbiology 2020 - “...promoters could be used depending on the environmental factors and growth conditions. For example, rpmH (CD3680) gene encoding 50S ribosomal protein L34 is associated with one SigF- and one SigA-dependent promoter having different deep-sequencing signal intensity for both 5-end RNA-seq and whole transcript RNA-seq ( Figure...”
- Temporal differential proteomes of Clostridium difficile in the pig ileal-ligated loop model
Janvilisri, PloS one 2012 - “...the numbering of the C. difficile 630 coding sequences, with CD0001 at the top and CD3680 at the bottom, followed by proteins from the plasmid pCD630 (CDP01 to CDP11). Each column represents a particular time point in one iTRAQ experiment, and each row corresponds to a...”
- “...ileal loops. Genes/proteins are ordered in rows beginning with CD0001 from the top down to CD3680, followed by CDP01-CDP11 at the bottom. Red and green colors indicate up- and down-regulation, respectively, compared to the control conditions. Grey denotes genes/proteins that are not differentially expressed. (B) Distance...”
- Array comparative hybridisation reveals a high degree of similarity between UK and European clinical isolates of hypervirulent Clostridium difficile
Marsden, BMC genomics 2010 - “...were arranged by their corresponding C. difficile 630 gene, with CD0001 at the top and CD3680 at the bottom, followed by CDS from the plasmid pCD630 (CDP01 to CDP11) and finally probes representing the genes unique to ribotype 027. Each column represents an isolate, and each...”
- Microarray identification of Clostridium difficile core components and divergent regions associated with host origin
Janvilisri, Journal of bacteriology 2009 - “...C. difficile 630 genes, with CD0001 at the top and CD3680 at the bottom, followed by CDS from the plasmid pCD630 (CDP01 to CDP11). Each column represents an...”
RL34_THET8 / P80340 Large ribosomal subunit protein bL34; 50S ribosomal protein L34 from Thermus thermophilus (strain ATCC 27634 / DSM 579 / HB8) (see paper)
5a9zAd / P80340 of Thermous thermophilus ribosome bound to BipA-GDPCP (see paper)
TTHA0446 ribosomal protein L34 from Thermus thermophilus HB8
62% identity, 92% coverage
- function: Found on the solvent side of the large subunit
subunit: Part of the 50S ribosomal subunit - Ligand: rna (5a9zAd)
- Discovering the DNA-Binding Consensus of the Thermus thermophilus HB8 Transcriptional Regulator TTHA1359
Teague, International journal of molecular sciences 2021 - “...sites upstream of the core promoter elements (e.g., TTHA0953 , TTHA0987 , TTHA0784 , and TTHA0446 ). However, most had TTHA1359 sites overlapping core promoter elements, either the 35 box (e.g., TTHA0425 , TTHA0447 , and TTHA0533 ) or the 10 box (e.g., TTHA0080 , TTHA0081...”
- “...TTHA1359-regulated genes were involved in universal processes, including transcription ( TTHA0953 ) and translation ( TTHA0446 , tRNA-Ala-3 , and TTHA0083 ). Notably, those genes involved in translation were present in different transcriptional units (operons), suggestive of their coordinate regulation by TTHA1359. Others were involved in...”
GOX1825 LSU ribosomal protein L34P from Gluconobacter oxydans 621H
66% identity, 96% coverage
5myjB6 / A2RHL6 of 70S ribosome from Lactococcus lactis (see paper)
L133770 50S ribosomal protein L34 from Lactococcus lactis subsp. lactis Il1403
64% identity, 96% coverage
- Ligand: rna (5myjB6)
- Strain-Dependent Transcriptome Signatures for Robustness in Lactococcus lactis
Dijkstra, PloS one 2016 - “...stress (A) or oxidative stress (B). A Strain Locus tag Gene Function Correlation Slope IL1403 L133770 rpmH 50S_ribosomal_protein_L34 negative 3.1 L127611 yveD hypothetical protein negative 0.6 L36850 ps104 prophage_ps1_protein_04 negative 0.1 L52686 ycfD hypothetical_protein negative 1.1 L52019 gntK gluconate_kinase positive 0.4 L18206 ysdB ABC transporter ATP...”
D7FBT9 Large ribosomal subunit protein bL34 from Helicobacter pylori (strain B8)
HP1447 ribosomal protein L34 (rpl34) from Helicobacter pylori 26695
61% identity, 96% coverage
8c972 / P0A7P5 Cryo-em captures early ribosome assembly in action (see paper)
100% identity, 59% coverage
ECH_0440 ribosomal protein L34 from Ehrlichia chaffeensis str. Arkansas
64% identity, 96% coverage
BLIJ_2570 50S ribosomal protein L34 from Bifidobacterium longum subsp. infantis ATCC 15697 = JCM 1222 = DSM
64% identity, 96% coverage
BL0642 50S ribosomal protein L34 from Bifidobacterium longum NCC2705
64% identity, 96% coverage
HMPREF0424_0046 ribosomal protein L34 from Gardnerella vaginalis 409-05
64% identity, 96% coverage
SCO3880 50S ribosomal protein L34 from Streptomyces coelicolor A3(2)
63% identity, 93% coverage
AKJ12_RS19625, XFF4834R_chr42980 50S ribosomal protein L34 from Xanthomonas arboricola pv. juglandis
Q05HP6 Large ribosomal subunit protein bL34 from Xanthomonas oryzae pv. oryzae (strain KACC10331 / KXO85)
81% identity, 93% coverage
TTE2802 Ribosomal protein L34 from Thermoanaerobacter tengcongensis MB4
61% identity, 96% coverage
XF_RS12125 50S ribosomal protein L34 from Xylella fastidiosa 9a5c
PD2123 50S ribosomal protein L34 from Xylella fastidiosa Temecula1
77% identity, 93% coverage
- Overexpression of mqsR in Xylella fastidiosa Leads to a Priming Effect of Cells to Copper Stress Tolerance
Carvalho, Frontiers in microbiology 2021 - “...argM or cstC ), and two hypothetical proteins (XF_RS03860, XF_RS05645). Interestingly though, the ribosomal protein (XF_RS12125) was the only one showing an opposite behavior, being induced in C-3/C-0 but suppressed in M-3/M-0. This protein is involved in translation, and accordingly, this category was downregulated in M-3/M-0....”
- Comparative Genomics of Xylella fastidiosa Explores Candidate Host-Specificity Determinants and Expands the Known Repertoire of Mobile Genetic Elements and Immunity Systems
Uceda-Campos, Microorganisms 2022 - “...S3 ), the lowest Smap values (~0.14) were for highly conserved CDSs such as ribosomal (PD2123) and cell division (PD1872) proteins. On the other hand, the highest Smap values found were ~0.5 belonging to CDSs encoding TonB-dependent receptor and the hypothetical protein PD0014 ( Table S3...”
- Csp1, a Cold Shock Protein Homolog in Xylella fastidiosa Influences Cell Attachment, Pili Formation, and Gene Expression
Wei, Microbiology spectrum 2021 - “...DNA transport competence protein 16,765.37 7,555.53 0.45 PD1709 mopB Outer membrane protein 597.52 309.74 0.52 PD2123 rpmH 50S ribosomal protein L34 36,412.20 19,544.34 0.54 PD0446 rpsQ 30S ribosomal protein S17 11,515.54 6,378.49 0.55 PD0451 rpsH 30S ribosomal protein S8 3,394.73 1,983.09 0.58 PD0060 fimD Outer membrane...”
- Characterization of regulatory pathways in Xylella fastidiosa: genes and phenotypes controlled by algU
Shi, Applied and environmental microbiology 2007 - “...rpsN rpsH 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...”
CPj0935 50S ribosomal protein L34 from Chlamydia pneumoniae J138
Q9Z6X1 Large ribosomal subunit protein bL34 from Chlamydia pneumoniae
CPj0935 L34 ribosomal protein from Chlamydophila pneumoniae J138
64% identity, 91% coverage
- Genome-wide analysis of Chlamydophila pneumoniae gene expression at the late stage of infection
Miura, DNA research : an international journal for rapid publication of reports on genes and genomes 2008 - “...CT145 Constitutive ND CPj0934 rnpA Ribonuclease P protein component Late Const. ND CT784 Constitutive ND CPj0935 rl34 L34 ribosomal protein Late Const. ND CT785 Constitutive ND CPj0577 SWIB (YM74) complex protein NL Const. ND CT460 Constitutive ND CPj0695 ompA Major outer membrane protein NL Const. Up...”
- “...at the late stage ( Table1 ). However, the other three genes, CPj0148, CPj0934, and CPj0935, were constitutive in the RTPCR analysis. The DNA fragment containing CPj0934 and CPj0935 for the DNA microarray also carries CPj0933, which is consistently categorized into the late gene (S14S17 in...”
- Prediction of Chlamydia pneumoniae protein localization in host mitochondria and cytoplasm and possible involvements in lung cancer etiology: a computational approach
Alshamsan, Saudi pharmaceutical journal : SPJ : the official publication of the Saudi Pharmaceutical Society 2017 - “...L10 (Q9Z9A2), L9 (Q9Z6V3), L4 (Q9Z7Q8), L5 (Q9Z7R9), L29 (Q9Z7R5), L27 (Q9Z807), L33 (Q9Z8T4), L34 (Q9Z6X1) and L35 (Q9Z6R8), L36 (Q9Z6X0), which potentially involved in various steps of translation and ribosome biogenesis in C. pneumoniae . Control of translation is a critical component for the progress...”
RPA0634 possible ribosomal protein L34 from Rhodopseudomonas palustris CGA009
73% identity, 96% coverage
- ATP Is a Major Determinant of Phototrophic Bacterial Longevity in Growth Arrest
Yin, mBio 2023 - “...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, RPA2768, RPA2922,...”
bsr8096 ribosomal protein L34 from Bradyrhizobium japonicum USDA 110
73% identity, 96% coverage
A8FJG4 Large ribosomal subunit protein bL34 from Bacillus pumilus (strain SAFR-032)
68% identity, 96% coverage
- Differentiation of Bacillus pumilus and Bacillus safensis using MALDI-TOF-MS
Branquinho, PloS one 2014 - “...c 3060 NA NA Unassigned NA NA 3608.5 NA NA Unassigned NA NA 5270 0.02 A8FJG4 50S b RP subunit L34 MKRTFQPNNRKRSKVHGFRSRMSSKNGRLVLKRRRSKGRKKLSA B. pumilus SAFR-032 5271 B. pumilus 5266.89 0.08 A8FDQ9 a SASP O MTKRKANHVINGMNAAKSQGNGAGYIEDDQLVLTAEQRQNNKKRKKNQ B. pumilus SAFR-032 6114 0.2 C0H3U0 Uncharacterized membrane protein YyzG MQTNRVILLAVMICLVSAITVFLLNGCKVDFLDIGGTIIGCFLGIFVVVRIQKKQS...”
MAB_4955c 50S ribosomal protein L34 from Mycobacterium abscessus ATCC 19977
58% identity, 91% coverage
- Genome-Wide Essentiality Analysis of Mycobacterium abscessus by Saturated Transposon Mutagenesis and Deep Sequencing
Rifat, mBio 2021 - “...uroporphyrin-III C-methyltransferase MAB_4145 Probable ,-trehalose-phosphate synthase MAB_4953c Membrane protein OxaA MAB_4954c Ribonuclease P protein component MAB_4955c 50S ribosomal protein L34 a Genes for hypothetical proteins: MAB_1062, MAB_1669, MAB_2403, MAB_2404, MAB_2751, MAB_2893c, MAB_4077, MAB_4318 (homologous to a M. avium gene), and MAB_4471. TABLE3 Essential M. abscessus genes...”
MSMEG_6946 ribosomal protein L34 from Mycobacterium smegmatis str. MC2 155
MSMEG_6946 50S ribosomal protein L34 from Mycolicibacterium smegmatis MC2 155
58% identity, 91% coverage
- MnoSR removal in Mycobacterium smegmatis triggers broad transcriptional response to 1,3-propanediol and glucose as sole carbon sources
Płocińska, Frontiers in cellular and infection microbiology 2024 - “...msmeg_1346, msmeg_1428, msmeg_2435, msmeg_2440, msmeg_2541, msmeg_2564, msmeg_4571, msmeg_4580, msmeg_4951, msmeg_5222, msmeg_5431, msmeg_5489, msmeg_6894, msmeg_6897 and msmeg_6946 . MnoRS weakly influences utilization of sugars as carbon sources and does not affect nitrogen metabolism Next, we ask the question of whether the up- or downregulation of genes related...”
- Elucidating the role of c-di-AMP in Mycobacterium smegmatis: Phenotypic characterization and functional analysis
Chaudhary, Heliyon 2023 - “...protein S18 2.05 0.048 2 rpmE (MSMEG_4951) 50S ribosomal protein L31 1.73 0.034 3 rpmH (MSMEG_6946) 50S ribosomal protein L34 1.13 0.031 4 rpsT (MSMEG_4571) 30S ribosomal protein S20 1.60 0.023 5 rplL (MSMEG_1365) 50S ribosomal protein L7/L12 2.43 0.027 6 rplI (MSMEG_6894) 50S ribosomal protein...”
- Gene Expression, Bacteria Viability and Survivability Following Spray Drying of Mycobacterium smegmatis
Lauten, Materials (Basel, Switzerland) 2010 - “...L33 rpmG -0.4 9.4 0.368 0% MSMEG_1339 ribosomal protein L33 rpmG 0.6 11.6 0.045 9% MSMEG_6946 ribosomal protein L34 rpmH 0.3 11.5 0.282 0% MSMEG_3792 ribosomal protein L35 rpmI 0.8 13.6 0.004 46% MSMEG_1520 ribosomal protein L36 rpmJ 0.4 13.3 0.080 1% MSMEG_3833 ribosomal protein S1...”
Rv3924c 50S ribosomal protein L34 from Mycobacterium tuberculosis H37Rv
MT4041.1 50S ribosomal protein L34 from Mycobacterium tuberculosis CDC1551
58% identity, 91% coverage
- Integrated sequence and -omic features reveal novel small proteome of Mycobacterium tuberculosis
Sinha, Frontiers in microbiology 2024 - “...var. africanum. In another instance, MTB_ORF_37415 is coupled with the start codon of rpmH ( Rv3924c ), and the presence of this peptide was also identified in the LC/MS-MS study ( Figure 4B ). Another example is MTB_ORF_12497, which is coupled with the start codon of...”
- “...potential translation coupling. (A) Coupling between MTB_ORF_2957 and Rv0280 ; (B) Coupling between MTB_ORF_37415 and Rv3924c ; and (C) Coupling between MTB_ORF_12497 and Rv1297 . Upstream open reading frames (uORFs) are the small protein-coding regions in mRNA that precede the main coding region of a gene....”
- HigB1 Toxin in Mycobacterium tuberculosis Is Upregulated During Stress and Required to Establish Infection in Guinea Pigs
Sharma, Frontiers in microbiology 2021 - “...protein Rv0056 rplI 2.24 Up 50S ribosomal protein L9 Rv2990c Rv2990c 2.24 Up Hypothetical protein Rv3924c rpmH 2.20 Up 50S ribosomal protein L34 Rv2254c Rv2254c 2.20 Up Integral membrane protein Rv1158c Rv1158c 2.19 Up Hypothetical protein Rv0634B rpmG2 2.17 Up 50S ribosomal protein L33 Rv1535 Rv1535...”
- “...levels of ribosomal proteins such as Rv0055, Rv0056, Rv0651, Rv0652, Rv0700, Rv0714, Rv0715, Rv0717, and Rv3924c were increased in the higB 1 mutant strain as compared to the wild type strain ( Table 1 ). Transcriptional profiling of ribosomal proteins and its associated proteins in higB...”
- Comparative proteomic analysis of sequential isolates of Mycobacterium tuberculosis sensitive and resistant Beijing type from a patient with pulmonary tuberculosis
Singh, International journal of mycobacteriology 2016 (PubMed)- “...wag31, Rv2714, GarA, SSB, FabG4, Probable lipase, Rv3924c, Rv3204A, Rv2031c, Rv3418c and GroES. The InterProScan and homology searches generated insights into...”
- Osmosensory signaling in Mycobacterium tuberculosis mediated by a eukaryotic-like Ser/Thr protein kinase
Hatzios, Proceedings of the National Academy of Sciences of the United States of America 2013 - “...Rv3460c Rv3613c Rv3614c Rv3615c Rv3616c Rv3763 Rv3810 Rv3924c MT0066.1 MT0066.2 MT0835 MT1178 MT1448 MT2245 MT2420 MT2421 MT2422 MT2460 MT2516 MT3217 MT3562...”
- Mycobacterium tuberculosis septum site determining protein, Ssd encoded by rv3660c, promotes filamentation and elicits an alternative metabolic and dormancy stress response
England, BMC microbiology 2011 - “...rpsM -1.3 -0.6 Rv0035 fadD34 1.3 0.0 Rv3461c rpmJ -1.4 -0.6 Rv0214 fadD4 0.8 -0.2 Rv3924c rpmH -1.2 -0.7 Rv0551c fadD8 0.9 0.0 Rv2590 fadD9 1.3 -0.5 Anaerobic respiration Rv0972c fadE12 1.4 -0.1 Rv0252 nirB 0.8 ndr Rv0975c fadE13 1.3 ndr Rv0253 nirD 1.1 ndr Rv3061c...”
- 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 - “...MT0114, MT0736, MT0728, MT0747, MT1337, MT2117.1, MT0663, MT4041.1, MT1680, MT3567.1, MT0729, MT0742, MT0744, MT0681, MT0062 Small subunit 22 MT1666, MT0727,...”
ML2713 50S ribosomal protein L34 from Mycobacterium leprae TN
56% identity, 91% coverage
wcw_0805 50S ribosomal protein L34 from Waddlia chondrophila WSU 86-1044
51% identity, 93% coverage
5mrcY / Q04598 of the yeast mitochondrial ribosome - Class A (see paper)
55% identity, 87% coverage
RM34_YEAST / Q04598 Large ribosomal subunit protein bL34m; 54S ribosomal protein L34, mitochondrial; L34mt from Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast) (see 4 papers)
YDR115W Putative mitochondrial ribosomal protein of the large subunit, has similarity to E. coli L34 ribosomal protein; required for respiratory growth, as are most mitochondrial ribosomal proteins from Saccharomyces cerevisiae
55% identity, 38% 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 yeast 74S mitochondrial ribosomes consist of a small (37S) and a large (54S) subunit. The 37S small subunit contains a 15S ribosomal RNA (15S mt-rRNA) and 34 different proteins. The 54S large subunit contains a 21S rRNA (21S mt-rRNA) and 46 different proteins. - Metabolic regulation of misfolded protein import into mitochondria
Wang, eLife 2024 - “...UBP14 Class 2 YBR175W SWD3 Class 2 YBR231C SWC5 Class 2 YDR073W SNF11 Class 2 YDR115W MRX14 Class 2 YGR136W LSB1 Class 2 YGR159C NSR1 Class 2 YHL033C RPL8A Class 2 YHR011W DIA4 Class 2 YHR143W DSE2 Class 2 YCL005W LDB16 Class 2 YCL037C SRO9 Class...”
- Saccharomyces cerevisiae responds similarly to co-culture or to a fraction enriched in Metschnikowia pulcherrima extracellular vesicles
Mejias-Ortiz, Microbial biotechnology 2023 - “...mitochondrial ribosomal proteins are mostly excluded of the overexpressed genes, with only six exceptions (YCR046C, YDR115W, YCR003W, YNL284C, YNR036C, and YGL068W), for M . pulcherrima living cells, or four exceptions (YCR046C, YDL202W, YDR115W, YGL068W, and YNR036C) for the EVenriched fraction, among the 35 genes labelled for...”
- The RNA fold interactome of evolutionary conserved RNA structures in S. cerevisiae
Casas-Vila, Nature communications 2020 - “...further supported by similar genetic interaction profiles (community 4) (Fig. 3e ). In another case, YDR115W clusters together with the mitochondrial ribosome-recycling factor RRF1 , perhaps suggesting a possible role for YDR115W in mitochondrial translation (community 13). As shown above, our integration with physical interactomics data...”
- Systematic analysis of nuclear gene function in respiratory growth and expression of the mitochondrial genome in S. cerevisiae
Stenger, Microbial cell (Graz, Austria) 2020 - “...MRP4 YHL004W MRPS8 YMR158W SLM5 YCR024C MRP51 YPL118W MRS1 YIR021W SLS1 YLR139C MRP7 YNL005C MRX14 YDR115W SWS2 YNL081C MRPL10 YNL284C MSD1 YPL104W TUF1 YOR187W MRPL11 YDL202W MSE1 YOL033W MRPL13 YKR006C MSF1 YPR047W Mitochondrial transcription MSS116 YDR194C MTF2 YDL044C MTF1 YMR228W RPO41 YFL036W Respiratory chain components and...”
- Mitochondrial ribosome bL34 mutants present diminished translation of cytochrome c oxidase subunits
Guedes-Monteiro, Cell biology international 2018 - “...mitoribosome biogenesis, here we characterize bL34 temperature sensitive mutants encoded in yeast by MRPL34 (ORF YDR115w). Mitoribosome bL34 associates with a specific mitoribosome protein mL41, involved in the stabilization of rRNA 16S helix 8-ES1, and uL29 present in the mitoribosome exit tunnel site ( Brown et...”
- “...to have the null allele by genetic crosses to a mutant with a deletion in YDR115w, obtained from the Genome Deletion strain collection and by specific diagnostic by PCR amplification. Construction of a temperature-sensitive allele of mrpl34 and site-directed mutagenesis MRPL34 was mutagenized by PCR amplification...”
- Integrating transcriptomics and metabolomics for the analysis of the aroma profiles of Saccharomyces cerevisiae strains from diverse origins
Mendes, BMC genomics 2017 - “...QCR9 RIP1 COB COX1 COX16 COX23 COX3 COX5A CYT1 MAM33 NDE1 NDI1 QCR8 QCR9 RIP1 YDR115W COX1 COX13 COX16 COX23 COX5A COX6 COX7 CYT1 MRPL1 NDI1 QCR10 QCR7 QCR8 QCR9 RIP1 YDR115W tetracyclic and pentacyclic triterpenes (cholesterin, steroids and hopanoids) metabolism ARE2 ERG1 ERG10 ERG13 ERG2...”
- “...MRPL44 MRPL6 MRPL8 MRPL9 MRPS16 MRPS28 NAM9 NDE1 NDI1 RML2 RSM18 RSM19 RSM25 RSM26 TIM10 YDR115W YMR31 CYB2 GET1 HSP10 MDM35 MDV1 MNP1 MRM2 MRP13 MRP2 MRP21 MRP49 MRPL1 MRPL10 MRPL13 MRPL20 MRPL23 MRPL27 MRPL32 MRPL35 MRPL36 MRPL37 MRPL38 MRPL39 MRPL40 MRPL44 MRPL49 MRPL6 MRPL9 MRPS16...”
- CAN1 Arginine Permease Deficiency Extends Yeast Replicative Lifespan via Translational Activation of Stress Response Genes
Beaupere, Cell reports 2017 - “...and mitochondrial and cytoplasmic ribosomal protein genes ( MRPL25, MRPS8, RPL29, RPL39, RPS29A, RPS30A, RRF1, YDR115W, YNL122C ). In contrast to can1 cells , a number of genes were activated at the level of translation in cells lacking TOR1 , whereas very few genes were down-regulated...”
- A Comprehensive Analysis of Replicative Lifespan in 4,698 Single-Gene Deletion Strains Uncovers Conserved Mechanisms of Aging
McCormick, Cell metabolism 2015 - “...components of the large subunit of mitochondrial ribosome; IMG1, IMG2, MRPL33, MRPL40, MRPL49 , and YDR115W . We also saw increased RLS upon deletion of the genes encoding 2 mitochondrial tRNA synthetases, MSK1 and MSW1 , and three mitochondrial translation control (MTC) genes, SOV1, SUV3 ,...”
- “...SOV1 31.29 16.8 YUR1 31.18 19.2 RPL20B 36.40 35.0 SUV3 33.82 21.8 RPL21B 36.93 49.5 YDR115W 30.13 11.7 RPL22A 36.59 38.4 RPL23A 34.02 31.9 TCA Cycle SAGA RPL26A 31.39 21.6 gene mean RLS % inc. gene mean RLS % inc. RPL29 32.08 31.9 EMI5 31.66 28.3...”
- More
PADG_04085 ribosomal protein L34 from Paracoccidioides brasiliensis Pb18
58% identity, 26% coverage
- Paracoccidioides spp.: the structural characterization of extracellular matrix, expression of glucan synthesis and associated genes and adhesins during biofilm formation
Oliveira, Frontiers in microbiology 2024 - “...in qRT-PCR. Oligonucleotide Sequence (5 3 ) Gene identification Fragment lenght References L34 F: TCAATCTCTCCCGCGAATCC PADG_04085 118 bp Goes et al., 2014 R: AGTTGGCGATTGTTGTGCGG ACT1 F: CGTCCTCGCCATCATGGTAT AY383732 142 bp de Curcio, 2018 R: TCTCCATATCATCCCAGTTCG ENOLASE F: CCTACCGTTGAGGTTGATGT EF558735.1 158 bp This study R: TTGACGTTCTTGACTGCGTTC 14-3-3...”
- Iron Deprivation Modulates the Exoproteome in Paracoccidioides brasiliensis
de, Frontiers in cellular and infection microbiology 2022 - “...was performed in triplicate for each cDNA. Normalization used the gene encoding the L34 protein (PADG_04085). The standard curve method for relative quantification was used for calculating the relative expression levels of transcripts of interest. Standard curve was obtained using an aliquot from each cDNA sample....”
- Metabolic Adaptation of Paracoccidioides brasiliensis in Response to in vitro Copper Deprivation
Petito, Frontiers in microbiology 2020 - “...in a Step OnePlus system (Applied Biosystems). Normalization used the gene encoding the L34 protein (PADG_04085). Standard curves were generated by 1:5 dilution of the cDNA, and the relative expression levels of the transcripts were calculated using the standard curve method for relative quantification ( Bookout...”
- “...normalized using the expression values of the transcript coding for L34 (GenBank accession number ( PADG_04085 ) Data are expressed as mean standard deviation from triplicates. *Statistically significant ( p < 0.05). Proteomic Analysis of Yeast Cells Submitted to in vitro Copper Deprivation Proteomic response of...”
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