PaperBLAST

PaperBLAST Hits for PFR28_05003 (73 a.a., MKTDIHPEYP...)

Show query sequence

>PFR28_05003
MKTDIHPEYPVVAVTCSCGNKFETRSTYGKALAIDVCNECHPFYTGKQKTLDTGGRVQKF
ADRFGAFGATKKA

Running BLASTp...

Found 114 similar proteins in the literature:

PP_5087 ribosomal protein L31 from Pseudomonas putida KT2440
83% identity, 97% 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
  • “...30S ribosomal protein S18 PP_4877 rpsF 30S ribosomal protein S6 PP_5027 dtD 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...”
  • “...S15 PP_4876 rpsR a 30S ribosomal protein 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...”

PFL_0441 ribosomal protein L31 from Pseudomonas fluorescens Pf-5
75% identity, 100% coverage

• Effect of tannic acid on the transcriptome of the soil bacterium Pseudomonas protegens Pf-5
  Lim, Applied and environmental microbiology 2013
  • “...(C form). In contrast, the transcript levels of PFL_0441, which encodes the zincbinding paralog (C form), were not influenced significantly by TA. The...”

Q9HUD0 Large ribosomal subunit protein bL31 from Pseudomonas aeruginosa (strain ATCC 15692 / DSM 22644 / CIP 104116 / JCM 14847 / LMG 12228 / 1C / PRS 101 / PAO1)
PA14_66710 50S ribosomal protein L31 from Pseudomonas aeruginosa UCBPP-PA14
PA5049 50S ribosomal protein L31 from Pseudomonas aeruginosa PAO1
66% identity, 97% coverage

• Top-Down LESA Mass Spectrometry Protein Analysis of Gram-Positive and Gram-Negative Bacteria
  Kocurek, Journal of the American Society for Mass Spectrometry 2017
  • “...24 h, 37 C Storage: 4 days, room temperature -Met 990.3747 +8 7914.94 -1.4 L31 Q9HUD0 31 996.4895 +14 13,936.75 -0.8 Azurin P00282 14 -signal peptide, disulfide 1029.1389 +7 7196.92 -0.6 L29 Q9HWE3 29 Incubation: 48 h, 37 C Sampled fresh 1090.1381 +5 5445.65 0.4 PA2146...”
• Elucidating Essential Genes in Plant-Associated Pseudomonas protegens Pf-5 Using Transposon Insertion Sequencing
  Fabian, Journal of bacteriology 2021 (secret)
• Gene Expression Profiling of <i>Pseudomonas aeruginosa</i> Upon Exposure to Colistin and Tobramycin
  Cianciulli, Frontiers in microbiology 2021
  • “...34.45 4.5 yhbC PA14_62780 Hypothetical protein 14.37 ND smpB PA14_63060 SsrA-binding protein 12.7 2.36 rpmE PA14_66710 50S ribosomal protein L31 316.32 ND prfH PA14_72200 Peptide chain release factor-like protein 491.76 5.65 rnpA PA14_73420 Ribonuclease P 164.46 16.33 Stringent response and toxin-antitoxin systems PA14_01510 PA14_01510 Hypothetical protein...”
• Strategies for Zinc Uptake in Pseudomonas aeruginosa at the Host-Pathogen Interface
  Wang, Frontiers in microbiology 2021
  • “...al., 2018 ). RpmE2 and RpmJ2 are homologous proteins of the 50S ribosomal proteins RpmE (PA5049) and RpmJ (PA4242) in P. aeruginosa ( Pederick et al., 2015 ). There are usually two forms of prokaryotic ribosomal proteins, the C + subtype that binds metal ions such...”
• Global Analysis of the Zinc Homeostasis Network in Pseudomonas aeruginosa and Its Gene Expression Dynamics
  Ducret, Frontiers in microbiology 2021
  • “...zrmD PA4834 Nicotianamine synthase C+/C paralogs dksA PA4723 Supressor protein dksA2 PA5536 Supressor protein rpmE PA5049 Ribosomal protein L31 rpmE2 PA3601 Ribosomal protein L31 rpmJ PA4242 Ribosomal protein L36 rpmJ2 PA3600 Ribosomal protein L36 Others PA2807 PA2807 Copper binding protein oprD PA0958 Outer membrane porin Zn...”
• Reverse diauxie phenotype in Pseudomonas aeruginosa biofilm revealed by exometabolomics and label-free proteomics
  Yung, NPJ biofilms and microbiomes 2019
  • “...NR NR NR RpmD PA4245 50S ribosomal protein L30 NR NR NR NR NR RpmE PA5049 50S ribosomal protein L31 NR NR NR NR NR RpsL PA4268 30S ribosomal protein S12 NR NR NR NR SecG PA4747 Preprotein translocase subunit NR NR NR NR NR TatA...”
• Bacterial fitness in chronic wounds appears to be mediated by the capacity for high-density growth, not virulence or biofilm functions
  Morgan, PLoS pathogens 2019
  • “...0 0.000 nt PA3480 - 399 0 0.000 nt PA1013 purC 345 0 0.000 nt PA5049 rpmE 317 0 0.000 nt PA0906 - 314 0 0.000 nt PA5365 phoU 308 0 0.000 nt PA3647 - 305 0 0.000 nt PA1548 - 281 0 0.000 nt PA3244...”
• Protein-to-mRNA ratios are conserved between Pseudomonas aeruginosa strains
  Kwon, Journal of proteome research 2014
  • “...the APEX method. Using KEGG pathway enrichment analysis, we identified ribosomal proteins (PA3745, PA4432, and PA5049) with significantly high protein-to-mRNA ratios. We also found that genes involved in terpenoid backbone biosynthesis (PA3627 and PA4557), nucleotide excision repair (PA1529 and PA4234), and one carbon (folate) metabolism (PA0944...”
• 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
  • “...PA4739 PA4740 PA4743 PA4847 PA4848 PA4880 PA4935 PA4944 PA5049 PA5054 PA5067 PA5069 PA5078 PA5117 PA5128 PA5276 PA5316 PA5355 PA5460 PA5490 PA5491 PA5555 PA5557...”
• Gene expression in Pseudomonas aeruginosa swarming motility
  Tremblay, BMC genomics 2010
  • “...ribosomal protein S9 1.8 PA4567 rpmA 50S ribosomal protein L27 1.5 PA4672 peptidyl-tRNA hydrolase 1.7 PA5049 rpmE 50S ribosomal protein L31 1.6 1 : Genes up-regulated in tendril tip vs. NS and up-regulated in tendril tip vs. center. 2 : Genes up-regulated in tendril tip vs....”
• Microarray analysis of Pseudomonas aeruginosa reveals induction of pyocin genes in response to hydrogen peroxide
  Chang, BMC genomics 2005
  • “...protein (Membrane proteins; Transport of small molecules) PA1228 2.8 0.008 Hypothetical protein (Hypothetical, unclassified, unknown) PA5049 ( rpmE ) 2.8 0.008 50S ribosomal protein (Translation, post-translational modification, degradation) PA2619 ( infA ) 2.7 0.008 Initiation factor (Translation, post-translational modification, degradation) PA4221 ( fptA ) 2.7 0.008...”
  • “...potABCD ), and (iii) ribosomal protein genes, PA4432 ( rpsL ), PA4563 ( rpsT ), PA5049 ( rpmE ), and PA5315 ( rpmG ). It is also interesting that putative cell division inhibitors such as PA0671 and PA3008, which are similar to E. coli sulA [...”

8cd1Le / Q9HUD0 8cd1Le (see paper)
65% identity, 93% coverage

• Ligand: rna (8cd1Le)

KF946_12560 50S ribosomal protein L31 from Idiomarina loihiensis
65% identity, 93% coverage

• Physiologic, Genomic, and Electrochemical Characterization of Two Heterotrophic Marine Sediment Microbes from the Idiomarina Genus
  Vinales, Microorganisms 2022
  • “...Cytochrome c/FTR1 family iron permease Cytoplasmic membrane (10.00) KF946_11525 KGF88_11325 Cytochrome c4 100/64 Periplasmic (10.00) KF946_12560 KGF88_12535 50S ribosomal protein L31 rpmE 97/70 Cytoplasmic (9.26) KF946_13430 EAL and GGDEF domain-containing protein Cytoplasmic membrane (7.88) KGF88_01265 dsbC family protein Periplasmic (9.76) KGF88_01425 Thioredoxin family protein Unknownmay have...”

VP0255 ribosomal protein L31 from Vibrio parahaemolyticus RIMD 2210633
62% identity, 99% coverage

• Insights into Vibrio parahaemolyticus CHN25 response to artificial gastric fluid stress by transcriptomic analysis
  Sun, International journal of molecular sciences 2014
  • “...2.7392 50S ribosomal protein L28 VP0265 ( rpmC ) Chn25_0256 2.5323 50S ribosomal protein L29 VP0255 ( rpmE ) Chn25_0246 5.0193 50S ribosomal protein L31 VP0186 ( rpmG ) Chn25_0182 7.2192 50S ribosomal protein L33 VP2030 ( rpsA ) Chn25_1918 3.9866 30S ribosomal protein S1 VP0263...”

KGF88_12535 50S ribosomal protein L31 from Idiomarina loihiensis
58% identity, 97% coverage

• Physiologic, Genomic, and Electrochemical Characterization of Two Heterotrophic Marine Sediment Microbes from the Idiomarina Genus
  Vinales, Microorganisms 2022
  • “...c/FTR1 family iron permease Cytoplasmic membrane (10.00) KF946_11525 KGF88_11325 Cytochrome c4 100/64 Periplasmic (10.00) KF946_12560 KGF88_12535 50S ribosomal protein L31 rpmE 97/70 Cytoplasmic (9.26) KF946_13430 EAL and GGDEF domain-containing protein Cytoplasmic membrane (7.88) KGF88_01265 dsbC family protein Periplasmic (9.76) KGF88_01425 Thioredoxin family protein Unknownmay have multiple...”

HSM_0533 50S ribosomal protein L31 from Histophilus somni 2336
HSM_0533 ribosomal protein L31 from Haemophilus somnus 2336
64% identity, 88% coverage

• Identification and initial characterization of Hfq-associated sRNAs in Histophilus somni strain 2336
  Subhadra, PloS one 2023
  • “...209 Y Y HSM_0521 HSM_0522 B [ 8 ] HS45 608001 608193 193 Y Y HSM_0533 HSM_0534 ND This work HS46 616791 617166 376 Y - HSM_0539 HSM_0540 A [ 8 ] HS47 617726 618078 352 Y - HSM_0539 HSM_0540 A [ 8 ] HS48 618122...”

FTN_0278 50S ribosomal protein L31 from Francisella tularensis subsp. novicida U112
63% identity, 92% coverage

• Importance of host cell arginine uptake in Francisella phagosomal escape and ribosomal protein amounts
  Ramond, Molecular & cellular proteomics : MCP 2015
  • “...each ribosomal protein Gene Gene name FTN_1562 FTN_0278 FTN_0262 FTN_0261 FTN_0249 FTN_0246 FTN_0245 FTN_0236 FTN_1571 FTN_1559 FTN_1289 FTN_0254 FTN_0251...”

Asuc_0525 ribosomal protein L31 from Actinobacillus succinogenes 130Z
59% identity, 97% coverage

• Transcriptome analysis and anaerobic C₄ -dicarboxylate transport in Actinobacillus succinogenes
  Rhie, MicrobiologyOpen 2018
  • “...3 , Table S4 , 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...”

APL_0982 50S ribosomal protein L31 from Actinobacillus pleuropneumoniae L20
64% identity, 88% coverage

• Actinobacillus pleuropneumoniae genes expression in biofilms cultured under static conditions and in a drip-flow apparatus
  Tremblay, BMC genomics 2013
  • “...APL_1494 APL_1665 APL_2011 APL_2025 APL_2026 Down-regulated APL_0226 APL_0333 APL_0615 APL_0630 APL_0644 APL_0682 APL_0771 APL_0903 APL_0967 APL_0982 APL_1136 APL_1169 APL_1292 APL_1388 APL_1450 APL_1474 APL_1558 APL_1597 APL_1759 APL_1782 APL_1962 Interestingly, APL_1494, which encodes the fine tangled pili,was down-regulated in the drip-flow biofilm and in bacteria attached to SJPL...”

FTL_1303 50S ribosomal protein L31 from Francisella tularensis subsp. holarctica
63% identity, 92% coverage

• Francisella tularensis LVS surface and membrane proteins as targets of effective post-exposure immunization for tularemia
  Chandler, Journal of proteome research 2015
  • “...Cyto(9.26) X ( 21 ) M, 21 T 35 50S ribosomal protein L31 (RpmE) e FTL_1303 NC(SP) Cyto(9.26) 30S ribosomal protein S16 (RpsP) e FTL_1738 Cyto(9.26) 25 pyruvate dehydrogenase, E1 component (AceE) FTL_0309 Cyto(9.97) Y ( 40 , 50 ) M 23 , 50 26 chitinase...”
• An improved vaccine for prevention of respiratory tularemia caused by Francisella tularensis SchuS4 strain
  Bakshi, Vaccine 2008
  • “...Bfr Bacteroferritin 2.447 (P<0.001) FTL_0359 PulG Type IV pili fiber building block protein 2.15 (P<0.001) FTL_1303 rpmE 50S Ribosomal protein L31 1.647 (P<0.01) a Results represent cumulative values from four replicate RNA samples prepared under identical conditions and are representative of two experiments conducted with identical...”

B7C60_RS02450 50S ribosomal protein L31 from Vibrio fujianensis
60% identity, 97% coverage

• Comparative Genomics and Transcriptomics Analyses Reveal a Unique Environmental Adaptability of Vibrio fujianensis
  Huang, Microorganisms 2020
  • “...expressed candidate genes involved in the ribosome pathway. Gene ID Gene Alias Substates Function Upregulated B7C60_RS02450 rpmE large subunit ribosomal protein L31 Translation B7C60_RS04755 rpsT small subunit ribosomal protein S20 Translation B7C60_RS05710 rpmG large subunit ribosomal protein L33 Translation B7C60_RS05715 rpmB large subunit ribosomal protein L28...”

VC2679 ribosomal protein L31 from Vibrio cholerae O1 biovar eltor str. N16961
60% identity, 97% coverage

• RadD Contributes to R-Loop Avoidance in Sub-MIC Tobramycin
  Negro, mBio 2019
  • “...degradation 245 55 4.4 0.010 Translation VC0443* d ksgA rRNA modification 215 13 16.3 0.019 VC2679 rpmE Ribosomal protein 513 39 13.3 0.075 VC0582 rsmI rRNA modification 387 44 8.7 0.019 VC2660* efp Translation elongation factor 222 41 5.4 0.019 Other VC0556* gshA Thiol redox system...”
• A systems biology approach to modeling vibrio cholerae gene expression under virulence-inducing conditions
  Kanjilal, Journal of bacteriology 2010
  • “...VC0435 VC0637 VC1640 VC2573 VC2586 VC2587 VC2592 VC2679 VC0819 VC1043 VC1159 VC2000 VC2447 Continued on following page Downloaded from http://jb.asm.org/ on...”
• Mining regulatory 5'UTRs from cDNA deep sequencing datasets
  Livny, Nucleic acids research 2010
  • “...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 transcriptional regulator CspA RLE0357(6) 27 VCA0184 Cold-shock DNA-binding domain-containing protein RLE0357(6) 28 VCA0933 Cold-shock domain-contain protein RLE0357(6) 29 VCA0819 Co-chaperonin GroES RLE0003(75)...”

HI0758 ribosomal protein L31 (rpL31) from Haemophilus influenzae Rd KW20
62% identity, 88% coverage

• Initial proteome analysis of model microorganism Haemophilus influenzae strain Rd KW20
  Kolker, Journal of bacteriology 2003
  • “...HI0880 HI0782 HI0779 HI0789 HI1630 HI0879 HI0951 HI0785 HI0796 HI0758 HI0158 HI0950 HI0998 HI1319m HI0798.1 550 252 236 207 167 131 157 131 131 119 130 125...”

ACIAD2210 50S ribosomal protein L31 from Acinetobacter sp. ADP1
58% identity, 97% coverage

• Prophage induction and differential RecA and UmuDAb transcriptome regulation in the DNA damage responses of Acinetobacter baumannii and Acinetobacter baylyi
  Hare, PloS one 2014
  • “...protein Neither 5.3 ACIAD3565 Conserved hypothetical protein Neither 4.6 ACIAD3649 Conserved hypothetical protein Neither 3.9 ACIAD2210 rpmE 50S ribosomal protein L31 Neither 3.6 ACIAD3535 raiA Stress response ribosomal inhibitor Neither 3.0 ACIAD1205 dps Stress response DNA-binding protein, starvation induced resistance to H 2 O 2 ,...”

SRIM_028075 50S ribosomal protein L31 from Streptomyces rimosus subsp. rimosus ATCC 10970
62% identity, 97% coverage

• Phosphoproteome Dynamics of Streptomyces rimosus during Submerged Growth and Antibiotic Production
  Šarić, mSystems 2022
  • “...phosphorylation sites (30S ribosomal proteins S16, SRIM_029570, and S17, SRIM_018535, and 50S ribosomal protein L31, SRIM_028075). This PTM most likely participates in attenuating protein synthesis during the SIII phase, as it was reported that ribosomal protein phosphorylation affects protein translation and decreases protein synthesis in Streptomyces...”

A0J47_RS02550, VDA_003390 50S ribosomal protein L31 from Photobacterium damselae subsp. damselae
58% identity, 95% coverage

• Low salinity activates a virulence program in the generalist marine pathogen Photobacterium damselae subsp. damselae
  Barca, mSystems 2023
  • “...4.73 2.24 1.70E-29 ChrI A0J47_RS07485 Small subunit ribosomal protein S1 RpsA 4.29 2.10 3.66E-195 ChrI A0J47_RS02550 50s ribosomal protein L31 RpmE 3.85 1.94 2.64E-102 ChrI A0J47_RS09500 50S ribosomal protein L25 RplY 4.71 2.24 0 ChrI Metabolism and transport A0J47_RS17020 Glutathione synthase GshB 38.42 5.26 0 ChrII...”
• Transcriptome changes in response to temperature in the fish pathogen Photobacterium damselae subsp. damselae: Clues to understand the emergence of disease outbreaks at increased seawater temperatures
  Matanza, PloS one 2018
  • “...membrane vitamin B12 receptor BtuB 3.0 9.66178E-20 ChrI VDA_001405 Uracil phosphoribosyltransferase 3.0 1.51133E-50 ChrI Translation VDA_003390 LSU ribosomal protein L31p 2.7 1.98928E-09 ChrI VDA_003099 Translation elongation factor Tu 2.6 3.07515E-36 ChrI VDA_002952 SSU ribosomal protein S21p 2.6 1.9713E-24 ChrI Virulence and antimicrobial resistance VDA_000110 Serum resistance...”

Alvin_3050 ribosomal protein L31 from Allochromatium vinosum DSM 180
64% identity, 88% coverage

• A comparative quantitative proteomic study identifies new proteins relevant for sulfur oxidation in the purple sulfur bacterium Allochromatium vinosum
  Weissgerber, Applied and environmental microbiology 2014
  • “...Alvin_2662 Alvin_2664 Alvin_2667 Alvin_2758 Alvin_2879 Alvin_3050 MsrA Peptide methionine sulfoxide reductase Sulfur relay protein, TusE/DsrC/DsvC family...”

SO4120, SO_4120 ribosomal protein L31 from Shewanella oneidensis MR-1
57% identity, 93% coverage

• Snapshot of iron response in Shewanella oneidensis by gene network reconstruction
  Yang, BMC genomics 2009
  • “...protein L9 (RplI) -- -- -- 1.33 0.50 0.69 1.29 -- -- 3.58 3.56 3.83 SO4120 ribosomal protein L31(RpmE) 0.39 0.35 0.36 0.29 0.44 0.26 2.68 2.51 3.68 6.47 4.22 6.00 Aerobic energy metabolism SO0343 2-methyl citrate dehydratase (AcnD) 1.19 0.99 0.86 2.23 3.53 8.22 1.14...”
• Whole proteome analysis of post-translational modifications: applications of mass-spectrometry for proteogenomic annotation
  Gupta, Genome research 2007
  • “...The latter Figure 1. The ribosomal protein L31 (SO_4120) is entirely covered by identified peptides (all pephypothesis, if confirmed, would open tides longer...”

MT1337 50S ribosomal protein L31 from Mycobacterium tuberculosis CDC1551
Rv1298 50S ribosomal protein L31 from Mycobacterium tuberculosis H37Rv
59% identity, 81% coverage

• Conserved codon composition of ribosomal protein coding genes in Escherichia coli, Mycobacterium tuberculosis and Saccharomyces cerevisiae: lessons from supervised machine learning in functional genomics
  Lin, Nucleic acids research 2002
  • “...MT2517, MT3052.2, MT2118, MT0114, MT0736, MT0728, MT0747, MT1337, MT2117.1, MT0663, MT4041.1, MT1680, MT3567.1, MT0729, MT0742, MT0744, MT0681, MT0062 Small...”
• Metabolic Changes of Mycobacterium tuberculosis during the Anti-Tuberculosis Therapy
  Bespyatykh, Pathogens (Basel, Switzerland) 2020
  • “...2093 samples, abundance of RpsL and seven other ribosome proteins (Rv0055, Rv0714, Rv0720, Rv0722, Rv0979A, Rv1298, and Rv2412) was lower compared to the parental strains. This finding may be related to the fact that ribosomal proteins can be targeted by anti-tuberculosis drugs [ 16 ], and,...”
• The effect of growth rate on pyrazinamide activity in Mycobacterium tuberculosis - insights for early bactericidal activity?
  Pullan, BMC infectious diseases 2016
  • “...L2 4.49 7.33 tRNA-Met tRNA-Met 4.68 6.35 Rv0703 P95051 50S ribosomal protein L23 4.29 6.16 Rv1298 P66187 50S ribosomal protein L31 1.65 6.13 tRNA-Leu tRNA-Leu 2.33 5.97 tRNA-Ser tRNA-Ser 4.08 5.88 Rv0710 P95058 30S ribosomal protein S17 1.65 5.43 tRNA-Pro tRNA-Pro 3.70 5.20 Rv0705 P0A5X4 30S...”
• Comprehensive Definition of the SigH Regulon of Mycobacterium tuberculosis Reveals Transcriptional Control of Diverse Stress Responses
  Sharp, PloS one 2016
  • “...sigE 169.052.2 Alternative RNA polymerase sigma factor SigE Rv1259 udgB 420.3184.3 Probable uracil DNA glycosylase Rv1298 rpmE 9.60.3 50S ribosomal protein L31 Rv1334 Mec 116.526.4 Possible hydrolase Rv1471 trxB1 76.732.6 Probable thioredoxin Rv1528c papA4 5.31.9 Probable conserved polyketide synthase associated protein Rv1801 PPE29 17.34.7 PPE family...”
• Transcriptional profile of Mycobacterium tuberculosis replicating in type II alveolar epithelial cells
  Ryndak, PloS one 2015
  • “...]. In addition, 5/36 genes encoding 50S ribosomal proteins (Rv0714- rplN , Rv0716- rplE , Rv1298- rpmE , Rv2441c- rpmA , Rv3456c- rplQ ) were upregulated by M . tb in type II AEC ( Table 4 ) while 16/36 are downregulated by M . tb...”
• Rapid restriction enzyme-free cloning of PCR products: a high-throughput method applicable for library construction
  Chaudhary, PloS one 2014
  • “...4. Rv1211 228 11.8 7/7 (100) Y 5. Rv1134 237 12.2 8/8 (100) Y 6. Rv1298 243 12.7 8/8 (100) Y 7. Rv1335 282 13.5 8/8 (100) Y 8. Rv1738 285 14.6 8/8 (100) Y 9. Rv0287 294 13.8 7/7 (100) Y 10. Rv2117 294 14.8...”
• CtpV: a putative copper exporter required for full virulence of Mycobacterium tuberculosis
  Ward, Molecular microbiology 2010
  • “...L9 rv0710 RpsQ 1.52 30S ribosomal protein S17 rv0719 RplF 1.65 50S ribosomal protein L6 rv1298 RpmE 2.11 50S ribosomal protein L31 rv1471 TrxB 1.89 Thioredoxin reductase rv2109c PrcA 2.13 Proteasome [alpha]-type subunit 1 rv3117 CysA3 1.61 Thiosulfate sulfurtransferase Metal substitution rv0247c 1.72 Probable succinate dehydrogenase...”
• The gene expression data of Mycobacterium tuberculosis based on Affymetrix gene chips provide insight into regulatory and hypothetical genes
  Fu, BMC microbiology 2007
  • “...rplW 6378 651 Rv0668 rpoC 3637 661 Rv3461c rpmJ 6349 379 Rv3849 - 3615 650 Rv1298 rpmE 6160 765 Rv1211 - 3606 386 Rv3418c groES 6017 1376 Rv2204c - 3605 594 Rv1177 fdxC 6004 569 Rv1310 atpD 3604 694 Rv0685 tuF 5895 438 Rv3281 - 3579...”
• Quantification of global transcription patterns in prokaryotes using spotted microarrays
  Sidders, Genome biology 2007
  • “...1,984 2'-Deoxyribonucleotide metabolism* 46 Rv2346c Rv2346c 1,937 Conserved hypotheticals 47 Rv3679 Rv3679 1,931 Anions* 48 Rv1298 rpmE 1,883 Ribosomal protein synthesis* 49 Rv0108c Rv0108c 1,837 Unknown 50 Rv2193 ctaE 1,793 Aerobic respiration* *Essential genes (TraSH) [26,27]. Surface polysaccharides, lipopolysaccharides, proteins and antigens. DNA replication, repair, recombination...”
  • “...vitro 25 Rv0700 rpsJ 1,693 1,148 In vitro 26 Rv1078 pra 1,643 971 - 27 Rv1298 rpmE 1,529 543 In vitro 28 Rv2840c Rv2840c 1,495 566 - 29 Rv1630 rpsA 1,491 439 In vitro 30 Rv0046c ino1 1,488 620 - 31 Rv1886c fbpB 1,464 1,168 -...”

RL31_STRCO / Q9K4E5 Large ribosomal subunit protein bL31; 50S ribosomal protein L31 from Streptomyces coelicolor (strain ATCC BAA-471 / A3(2) / M145) (see paper)
SCO5359 50S ribosomal protein L31 from Streptomyces coelicolor A3(2)
59% identity, 97% coverage

• function: Binds the 23S rRNA.
  cofactor: Zn(2+) (Binds 1 zinc ion per subunit.)
  subunit: Part of the 50S ribosomal subunit.
• Conservation of thiol-oxidative stress responses regulated by SigR orthologues in actinomycetes
  Kim, Molecular microbiology 2012
  • “...lon ATP-dependent protease (S1) 6 SCO5357 * rho Transcription termination factor, an RNADNA helicase 3 SCO5359 * rpmE1 Ribosomal proteins L31 (S1, A) 3 SCO5360 prfA Peptide release factor A 3 SCO5361 hemK Probable release factor-specific methyltransferase 8 SCO5465 * Conserved hypothetical, probable F420-dependent NADP oxidoreductase...”
  • “...Sa, F, St, Ac, T, N, Ki, J, Mi, L, Cl, B, Ac (18/22) 37 SCO5359 * rpmE1 Ribosomal proteins L31 My, Rh, Sc, Sa, F, St, T, N, Ki, J (10/22) 723 SCO4609 htpX Possible peptidase, M. tuberculosis HtpX homologue, no SigR target, a SigE...”
• Comparative genomics of Streptomyces avermitilis, Streptomyces cattleya, Streptomyces maritimus and Kitasatospora aureofaciens using a Streptomyces coelicolor microarray system
  Hsiao, Antonie van Leeuwenhoek 2008
  • “...protein L13 0.27 0.45 0.50 0.40 SCO4735 30S ribosomal protein S9 0.36 0.02 0.00 0.01 SCO5359 50S ribosomal protein L31 0.86 0.22 1.40 0.46 SCO5564 putative 50S ribosomal protein L28 0.60 0.28 0.21 0.51 SCO5591 30S ribosomal protein S16 0.44 0.03 0.57 0.60 SCO5595 50S ribosomal...”
• The zinc-responsive regulator Zur controls a zinc uptake system and some ribosomal proteins in Streptomyces coelicolor A3(2)
  Shin, Journal of bacteriology 2007
  • “...were found in the S. coelicolor genome, rpmE1 (SCO5359), rpmE2 (SCO3427), and rpmE3 (SCO1150) (6). The rpmE1 gene contains the zinc-binding motif (the gene...”
  • “...numberb Cysteine motifc Proposed regulator L31 rpmE1 rpmE2 rpmE3 SCO5359 SCO3427 SCO1150 R Zur NDd L33 rpmG1 rpmG2 rpmG3 SCO4635 SCO3428 SCO0570 NDd Zur R a For...”
• Zinc-responsive regulation of alternative ribosomal protein genes in Streptomyces coelicolor involves zur and sigmaR
  Owen, Journal of bacteriology 2007
  • “...L31 rpsN1 (SCO4715) rpsR1 (SCO3908) rpmB1 (SCO5564) rpmE1 (SCO5359) L32 L33 rpmF1 (SCO5571) rpmG1 (SCO4635) L36 rpmJ1 (SCO4726) rpsN2 (SCO3430) rpsR2 (SCO3425)...”

SEN3886 50S ribosomal protein L31 from Salmonella enterica subsp. enterica serovar Enteritidis str. P125109
P66191 Large ribosomal subunit protein bL31 from Salmonella typhimurium (strain LT2 / SGSC1412 / ATCC 700720)
55% identity, 95% coverage

• Global transcriptomic analysis of ethanol tolerance response in Salmonella Enteritidis
  He, Current research in food science 2022
  • “...S7 SEN3260 rpmC 3.70 50S ribosomal protein L29 SEN3253 rplF 3.02 50S ribosomal protein L6 SEN3886 rpmE 3.41 50S ribosomal protein L31 SEN3266 rplW 3.64 50S ribosomal protein L23 SEN3276 rpsL 3.01 30S ribosomal protein S12 SEN3118 rpsO 4.51 30S ribosomal protein S15 SEN4160 rplL 3.54...”
• 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 ND ND ND ND ND ND -9.619 2.532 50S ribosomal protein L31 P66191 rpmE Translation ND ND ND ND ND ND 10.159 1.074 ND ND 50S ribosomal protein L33 P0A7P2 rpmG Translation ND ND 8.313 2.037 ND ND 7.849 1.076 ND ND 50S...”

RpmE / b3936 50S ribosomal subunit protein L31 from Escherichia coli K-12 substr. MG1655 (see 22 papers)
rpmE / P0A7M9 50S ribosomal subunit protein L31 from Escherichia coli (strain K12) (see 26 papers)
RL31_ECOLI / P0A7M9 Large ribosomal subunit protein bL31; 50S ribosomal protein L31 from Escherichia coli (strain K12) (see 8 papers)
5akaZ / P0A7M9 Em structure of ribosome-srp-ftsy complex in closed state (see paper)
b3936 50S ribosomal subunit protein L31 from Escherichia coli str. K-12 substr. MG1655
NP_418371 50S ribosomal subunit protein L31 from Escherichia coli str. K-12 substr. MG1655
Z5484 50S ribosomal subunit protein L31 from Escherichia coli O157:H7 EDL933
Z_RS25730 50S ribosomal protein L31 from Escherichia coli O157:H7 str. EDL933
54% identity, 95% coverage

• function: Binds the 23S rRNA.
  cofactor: Zn(2+) (Binds 1 zinc ion per subunit. Only 1 ligand appears to be Cys, the other are thought to be His and either backbone amides or solvent (PubMed:22196016).)
  subunit: Part of the 50S ribosomal subunit.
• Ligand: rna (5akaZ)
• The Gene Expression Profile of Uropathogenic Escherichia coli in Women with Uncomplicated Urinary Tract Infections Is Recapitulated in the Mouse Model
  Frick-Cheng, mBio 2020
  • “...glucans 2.6 b1047 ribE 6,7-Dimethyl-8-ribityllumazine synthase 2.1 b0415 rpmE 50S ribosomal subunit protein L31 2.7 b3936 suhB Inositol phosphate phosphatase 2.6 b2533 yajG Putative lipoprotein YajG 2.6 b0434 yceA UPF0176 protein YceA 3.5 b1055 yciB Inner membrane protein 2.3 b1254 ydiE PF10636 family protein YdiE 2.1...”
• 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
  • “...Annotation b3309 rplX 0.66 50S ribosomal protein L24 b3341 rpsG 0.66 30S ribosomal protein S7 b3936 rpmE 0.66 50S ribosomal subunit protein L31 b2609 rpsP 0.66 30S ribosomal protein S16 b1892 flhD 0.66 transcriptional activator FlhD b4202 rpsR 0.65 30S ribosomal protein S18 b3310 rplN 0.65...”
• Analysis of promoter targets for Escherichia coli transcription elongation factor GreA in vivo and in vitro
  Stepanova, Journal of bacteriology 2007
  • “...suppressor typAc rpmE rplK rplA rplJ rplL rpoB rpoC b3871 b3936 b3983 b3984 b3985 b3986 b3987 b3988 1.8 3.4 3.2 2.5 2 1.9 1.9 2 GTP-binding protein; predicted...”
• Phenotypic effects of paralogous ribosomal proteins bL31A and bL31B in E. coli.
  Lilleorg, Scientific reports 2020
  • GeneRIF: Phenotypic effects of paralogous ribosomal proteins bL31A and bL31B in E. coli.
• The Intersubunit Bridge B1b of the Bacterial Ribosome Facilitates Initiation of Protein Synthesis and Maintenance of Translational Fidelity.
  Lilleorg, Journal of molecular biology 2017 (PubMed)
  • GeneRIF: The authors conclude that the only protein-protein intersubunit bridge of the bacterial ribosome facilitates translation initiation and is essential for maintaining the reading frame of mRNA translation.
• Characterization of Zn(II)-responsive ribosomal proteins YkgM and L31 in E. coli.
  Hensley, Journal of inorganic biochemistry 2012
  • GeneRIF: Data show that maltose binding protein (MBP)-YkgM does not bind Zn(II), on the other hand, MBP-L31 tightly binds 1 equivalent of Zn(II).
• Primary structure of Escherichia coli ribosomal protein L31.
  Brosius, Biochemistry 1978 (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 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 4.15E08 P60438 Ribosomal subunit protein L3 rplC 0.29 4.88E09 P0A7M6 Ribosomal subunit protein L29 rpmC 0.3...”
• The Discovery of Ribosomal Protein bL31 from Escherichia coli: A Long Story Revisited
  Wada, International journal of molecular sciences 2023
  • “...of intact and short bL31s. The amino acid sequence of intact bL31 (70 amino acids) (P0A7M9 RL31_ECOLI, Uni Prot) is shown at the top, with amino acids 162 and 6370 shown in red and pink, respectively. Short bL31 (62 amino acids), shown in red at the...”
• Capturing Membrane Protein Ribosome Nascent Chain Complexes in a Native-like Environment for Co-translational Studies
  Pellowe, Biochemistry 2020
  • “...RL23, P0ADZ0; RL24, P60624; RL25, P68919; RL27, P0A7M0; RL28, P0A7M2; RL29, P0A7M6; RL30, P0AG51; RL31, P0A7M9; RL32, C4ZS29; RL33, P0A7N9; RL34, P0A7P6; RL35, P0A7Q2; RL36, P0A7Q7. Author Contributions G.A.P., E.R., and P.J.B. designed the research. G.A.P., H.E.F., K.L., T.M.G., and E.R. performed all experiments and analyses,...”
• A Helping Hand to Overcome Solubility Challenges in Chemical Protein Synthesis.
  Jacobsen, Journal of the American Chemical Society 2016
  • “...target via NCL. Here, we selected the L31 protein from E. coli . L31 (Uniprot P0A7M9, RL31_ECOLI) is a 70-residue protein within the large ribosomal subunit. 68 , 69 The synthesis strategy for preparing L31 entailed three peptide segments (L31-1, 2 and 3), including Lys 23...”
• Disruption of rcsB by a duplicated sequence in a curli-producing Escherichia coli O157:H7 results in differential gene expression in relation to biofilm formation, stress responses and metabolism
  Sharma, BMC microbiology 2017
  • “...subunit alpha +2.12 1.2E-03 Protein metabolism yaeJ Z0203 Peptidyl-tRNA hydrolase domain-containing protein 1.36 0.03 rpmE Z5484 50S ribosomal protein L31 2.20 0.019 pepA Z5872 Leucyl aminopeptidase 1.58 0.02 DNA/RNA metabolism hisT Z3580 tRNA pseudouridine synthase A 1.51 0.02 deoD Z5986 Purine nucleoside phosphorylase 1.37 0.04 mazG...”
• Transcriptomic Analysis of Viable but Non-Culturable Escherichia coli O157:H7 Formation Induced by Low Temperature
  Zhong, Microorganisms 2019
  • “...rpl R, rpl D, rpl V, Z_RS16205, rps C, rpl C, rpl W, rpmC , Z_RS25730, rpl X, Z_RS25530, rps I, rpl M, rps E, rpm A, rpl P, rps K, rpm G, rpl E, rpmI , rps G, rps S, rpm D, Z_RS20780, rps J,...”

NP_709740 50S ribosomal subunit protein L31 from Shigella flexneri 2a str. 301
54% identity, 95% coverage

• Computational Identification of Essential Enzymes as Potential Drug Targets in Shigella flexneri Pathogenesis Using Metabolic Pathway Analysis and Epitope Mapping
  Narad, Journal of microbiology and biotechnology 2021
  • “...protein L29 Cytoplasm No Hits 16 NP_709090 50S ribosomal protein L30 Cytoplasm No Hits 17 NP_709740 50S ribosomal protein L31 Cytoplasm No Hits 18 NP_707005 50S ribosomal protein L32 Cytoplasm No Hits 19 NP_709497 50S ribosomal protein L34 Cytoplasm No Hits 20 NP_707397 50S ribosomal protein...”

y0299 50S ribosomal protein L31 from Yersinia pestis KIM
YPO0111 50S ribosomal protein L31 from Yersinia pestis CO92
YPTB0102 50S ribosomal protein L31 from Yersinia pseudotuberculosis IP 32953
55% identity, 97% coverage

• Comparative Global Gene Expression Profiles of Wild-Type Yersinia pestis CO92 and Its Braun Lipoprotein Mutant at Flea and Human Body Temperatures
  Galindo, Comparative and functional genomics 2010
  • “...protein L18 rplR Protein synthesis 8.7 YPO0218 50S ribosomal protein L29 rpmC Protein synthesis 11.6 y0299 50S ribosomal subunit protein L31 rpmE Protein synthesis 15.1 Transport YPO2672 putative urea transporter Transport and binding proteins 33.3 YPO3156 ATP-dependent Clp protease ATP-binding subunit ClpX lopC Carbohydrate transport 29.3...”
• Characterization of Zur-dependent genes and direct Zur targets in Yersinia pestis
  Li, BMC microbiology 2009
  • “...Zur under zinc-deficient conditions [ 35 ]. The paralogous pairs of L31 protein are RpmE (YPO0111) and YkgM (YPO3134) in Y. pestis , while those of L36 protein are RpmJ (YPO0230) and RpmJ2 (YPO3135) [ 17 ]. YkgM and RpmJ2 are the C- forms of corresponding...”
• Tissue dual RNA-seq allows fast discovery of infection-specific functions and riboregulators shaping host-pathogen transcriptomes
  Nuss, Proceedings of the National Academy of Sciences of the United States of America 2017
  • “...sites in contrast to their paralogs encoded by YPTB0102 (RpmE) and YPTB3677 (RpmJ). Recent studies in E. coli and Bacillus subtilis suggested that the...”
• IscR is essential for yersinia pseudotuberculosis type III secretion and virulence
  Miller, PLoS pathogens 2014
  • “...(33) YPTB0017 secreted thiol:disulfide interchange protein dsbA 2.0 YPTB0097 ATP-binding heat shock protein hslU 2.7 YPTB0102 50S ribosomal protein L31 rpmE 2.4 YPTB0276 elongation factor Tu tuf 2.7 YPTB0279 50S ribosomal protein L11 rplK 2.5 YPTB0280 50S ribosomal protein L1 rplA 2.3 YPTB0281 50S ribosomal protein...”

EAMY_0136 50S ribosomal protein L31 from Erwinia amylovora CFBP1430
54% identity, 95% coverage

• The stringent response regulator (p) ppGpp mediates virulence gene expression and survival in Erwinia amylovora
  Yang, BMC genomics 2020
  • “..., ribosomal protein L3 1.17 11.07 EAMY_3385 rplD , ribosomal protein L4 1.15 10.38 rpm EAMY_0136 rpmE , ribosomal protein L31 2.64 9.97 EAMY_0078 rpmG , ribosomal protein L33 2.43 10.07 EAMY_3368 rpmD , ribosomal protein L30 1.8 10.52 EAMY_0077 rpmB , ribosomal protein L28 1.76...”

MSMEG_4951 50S ribosomal protein L31 from Mycolicibacterium smegmatis MC2 155
MSMEG_4951 ribosomal protein L31 from Mycobacterium smegmatis str. MC2 155
58% identity, 87% coverage

• Elucidating the role of c-di-AMP in Mycobacterium smegmatis: Phenotypic characterization and functional analysis
  Chaudhary, Heliyon 2023
  • “...1 Ribosome structure and function rpsR2 (MSMEG_6895) 30S ribosomal 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...”
• 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_4624-4625 as well as isolated ORFs msmeg_1339, 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...”
• Construction and Use of Transposon <i>MycoTetOP</i> ² for Isolation of Conditional Mycobacteria Mutants
  Riggs-Shute, Frontiers in microbiology 2019
  • “...essential for bacterial viability ( Ji, 2016 ). The insertion at locus V occurred in MSMEG_4951, which encodes the ribosomal protein L31. MSMEG_4950 and MSMEG_4949 immediately downstream encodes the protein chain release factor PrfA ( Rodnina, 2018 ) and its modifying enzyme HemK ( Yang et...”
• Monitoring global protein thiol-oxidation and protein S-mycothiolation in Mycobacterium smegmatis under hypochlorite stress
  Hillion, Scientific reports 2017
  • “...B 35,7 40,3 74,5 26,5 41,8 70,4 52 B 36,8 42,7 76,9 24,8 48,3 74,2 MSMEG_4951 rpmE 50S ribosomal protein L31 16* B 20,2 22,2 39,6 14,5 22,4 32,9 MSMEG_6895 rpsR2 30S ribosomal protein S18-2 20* B 24,6 73,6 84,8 8,9 76,0 84,9 57* (MSH;Cys) B...”
• Gene Expression, Bacteria Viability and Survivability Following Spray Drying of Mycobacterium smegmatis
  Lauten, Materials (Basel, Switzerland) 2010
  • “...L29 rpmC 1.8 11.8 0.013 14% MSMEG_1473 ribosomal protein L30 rpmD 1.5 11.9 0.001 95% MSMEG_4951 ribosomal protein L31 rpmE 0.8 13.8 0.005 37% MSMEG_5489 ribosomal protein L32 rpmF 1.1 11.1 0.010 22% MSMEG_6070 ribosomal protein L31 rpmE 0.0 10.1 0.704 0% MSMEG_6067 ribosomal protein L33...”

5zeb2 / A0R215 5zeb2 (see paper)
58% identity, 89% coverage

• Ligand: rna (5zeb2)

MAB_1441 50S ribosomal protein L31 from Mycobacterium abscessus ATCC 19977
56% identity, 88% coverage

• Mycobacterium abscessus extracellular vesicles increase mycobacterial resistance to clarithromycin in vitro
  Vermeire, Proteomics 2024 (secret)

9c4g4 / A0A2B7JUW7 Cutibacterium acnes 50s ribosomal subunit with clindamycin bound (see paper)
59% identity, 89% coverage

• Ligand: zinc ion (9c4g4)

NMB1956 50S ribosomal protein L31 from Neisseria meningitidis MC58
NMA0495 50S ribosomal protein L31 from Neisseria meningitidis Z2491
61% identity, 89% coverage

• The zinc-responsive regulon of Neisseria meningitidis comprises 17 genes under control of a Zur element
  Pawlik, Journal of bacteriology 2012
  • “...of N. meningitidis r-proteins L31 and L36 are NMB1956 (C)/ NMB0942 (C) and NMB0164 (C)/NMB0941 (C), respectively (34, 51). The nmb0942-nmb0941 (rpmEJ) operon...”
• The transposon-like Correia elements encode numerous strong promoters and provide a potential new mechanism for phase variation in the meningococcus
  Siddique, PLoS genetics 2011
  • “...tandem hypothetical inner membrane protein 10 ---------------------------ga RS-dRS3 repeat array & another CE 11 ---------------------------ca NMA0495 ( rpmE ) 107 tandem 50S ribosomal protein L31 12 ---------------------------gt NMA0530A & NMA0531 4 , 5 259 convergent possible pseudogene & putative transposase 5 13 ---------------------------ac NMA0590 282 tandem...”

RB9304 50S ribosomal protein L31 from Pirellula sp. 1
RB9304 50S ribosomal protein L31 from Rhodopirellula baltica SH 1
58% identity, 81% coverage

• Life cycle analysis of the model organism Rhodopirellula baltica SH 1(T) by transcriptome studies
  Wecker, Microbial biotechnology 2010
  • “...belonging to the ribosomal machinery (RB12197, RB2543, RB264, RB5801, RB5804, RB7022, RB7818, RB8253, RB8725 and RB9304), transcription regulation (RB10339, RB10458, RB11223, RB12372 and RB1392) and DNA replication and recombination (RB11863 and RB3281) in the late stationary phase, probably due to reduced growth activity. Additionally, the organism...”

GSU3107 ribosomal protein L31 from Geobacter sulfurreducens PCA
52% identity, 89% coverage

• Global transcriptional analysis of Geobacter sulfurreducens under palladium reducing conditions reveals new key cytochromes involved
  Hernández-Eligio, Applied microbiology and biotechnology 2020 (PubMed)
  • “...as c-type cytochromes GSU1062, GSU2513, GSU2808, GSU2934, GSU3107, OmcH, OmcM, PpcA, and PpcD under Pd(II)-reducing conditions. pilA and pilR mutant strains...”
  • “...Cytochrome c family protein, 9 heme-binding sites GSU3107 Ribosomal protein L31, 1 heme-binding site GSU2883 Cytochrome c family protein, 18 heme-binding...”
• Global transcriptional analysis ofGeobacter sulfurreducensunder palladium reducing conditions reveals new key cytochromes involved
  Hernández-Eligio, 2018
• Evolution of electron transfer out of the cell: comparative genomics of six Geobacter genomes
  Butler, BMC genomics 2010
  • “...protein PilB 39997632 GSU2537 0.90 arginine decarboxylase 39996434 GSU1332 0.90 heavy metal efflux pump 39998197 GSU3107 0.90 ribosomal protein L31 39997384 GSU2286 0.90 enolase 39996898 GSU1799 0.90 aspartate kinase 39997946 GSU2854 0.90 50S ribosomal protein L2 39995201 GSU0090 0.90 heterodisulfide reductase subunit 39998045 GSU2954 0.90 arsenical-resistance...”

Dde_2982 Ribosomal protein L31 from Desulfovibrio desulfuricans G20
43% identity, 93% coverage

• Shotgun proteomic analysis of nanoparticle-synthesizing Desulfovibrio alaskensis in response to platinum and palladium
  Capeness, Microbiology (Reading, England) 2019
  • “...Meta and HslJ 0.54 Dde_2637 Ribosomal protein L35 0.51 Dde_4007 50S ribosomal protein L32 0.31 Dde_2982 Ribosomal protein L31 0.66 Dde_1095 Ribosomal protein L19 0.52 Dde_0492 Hypothetical protein Dde_0492 0.45 Cell integrity/maintenance Dde_0327 Response regulator receiver protein 0.55 Dde_2249 Ribosomal protein L29 0.47 Dde_1413 Organic solvent...”

Cj0155c 50S ribosomal protein L31 from Campylobacter jejuni subsp. jejuni NCTC 11168
48% identity, 89% coverage

• Parallel evolution of genome structure and transcriptional landscape in the Epsilonproteobacteria
  Porcelli, BMC genomics 2013
  • “...leaderless cj0153c gene and the leadered H. pylori hp0553 ortholog. The dRNA-seq profiles for the cj0155c - cj0151c and hp0551 - hp0555 genes show that cj0153c gene has a TSS with a 70 -10 sequence, whereas hp0551 - hp0555 is transcribed as a single multicistronic mRNA,...”
• Culture of Campylobacter jejuni with sodium deoxycholate induces virulence gene expression
  Malik-Kale, Journal of bacteriology 2008
  • “...Cj0008 Cj0037c Cj0040 Cj0073c Cj0080 Cj0100 Cj0114 Cj0155c Cj0179 Cj0181 Cj0188c Cj0189c Cj0190c Cj0193c Cj0199c Cj0207 Cj0237 Cj0246c Cj0247c Cj0295 Cj0301c...”

CBO0135 50S ribosomal protein L31 from Clostridium botulinum A str. ATCC 3502
55% identity, 88% coverage

• Gene expression profiling of Clostridium botulinum under heat shock stress
  Liang, BioMed research international 2013
  • “...to 45C. Several genes involved in ribosomal protein synthesis and modification were downregulated, including rpmE (CBO0135), rplR (CBO3465), rplO (CBO3462), rplX (CBO3470), rpsQ (CBO3472), rpsN (CBO3468), rpsC (CBO3474), and rplK (CBO3492). The downregulation of ribosomal genes indicated a temporary growth arrest, allowing the bacteria to reshuffle...”

YSS_RS08510 50S ribosomal protein L31 from Campylobacter coli RM4661
48% identity, 89% coverage

• Proteotyping as alternate typing method to differentiate Campylobacter coli clades
  Emele, Scientific reports 2019
  • “...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 RpsT/S20 GCTCTTCTTCGAGTTTGGGTT GGTGGATTGGGTGTTATGCT 765 YSS_RS04540 RpsO/S15 ATATCGGATACAACCGCGCA GCATACTCGCTAGCTTTGGT 636 YSS_RS09430...”

CD3486A 50S ribosomal protein L31 from Clostridium difficile 630
50% identity, 88% coverage

• Semiquantitative analysis of clinical heat stress in Clostridium difficile strain 630 using a GeLC/MS workflow with emPAI quantitation
  Ternan, PloS one 2014
  • “...The most abundant protein in the 41C proteome by molar % was Ribosomal protein L31 (CD3486A), a component of the large 50S ribosomal subunit that contains four conserved cysteine residues that allow it to rapidly form intracellular disulfide bonds in vitro . Furthermore, the protein contains...”
• Temporal differential proteomes of Clostridium difficile in the pig ileal-ligated loop model
  Janvilisri, PloS one 2012
  • “...of ribosomal proteins such as RpmG (CD0058A), RpsN (CD0084A), RplU (CD1161), RpmF (CD1176A), and RpmE (CD3486A) that formed a tight interaction network as seen in the protein-protein interaction map ( Figure S1 ). Since genes encoding ribosomal proteins in C. difficile are clustered into operons with...”

LIC12637 50S ribosomal protein L31 from Leptospira interrogans serovar Copenhageni str. Fiocruz L1-130
49% identity, 88% coverage

• Global transcriptomic response of Leptospira interrogans serovar Copenhageni upon exposure to serum
  Patarakul, BMC microbiology 2010
  • “...ribosomal protein S18 - - LIC12865 (LA0747) rpmC -1.91 50S ribosomal protein L29 - - LIC12637 (LA1020) rpmE -1.88 50S ribosomal protein L31 - - LIC10750 (LA3423) rplA -1.82 50S ribosomal protein L1 - - LIC12862 (LA0750) rplX -1.75 50S ribosomal protein L24 - - LIC12113...”

TP0255 ribosomal protein L31 (rpmE) from Treponema pallidum subsp. pallidum str. Nichols
46% identity, 93% coverage

• Structural characterization of Treponema pallidum Tp0225 reveals an unexpected leucine-rich repeat architecture
  Ramaswamy, Acta crystallographica. Section F, Structural biology communications 2019
  • “...A multiple sequence alignment (MSA) of Tp0255 LRR-domain orthologs was generated using Clustal Omega (https://www.ebi.ac.uk/Tools/msa/clustalo/). A phylogenetic...”

RL31_BACSU / Q03223 Large ribosomal subunit protein bL31; 50S ribosomal protein L31 from Bacillus subtilis (strain 168) (see 3 papers)
BSU37070 50S ribosomal protein L31 from Bacillus subtilis subsp. subtilis str. 168
46% identity, 89% coverage

• function: Binds the 23S rRNA.
  function: While neither of the L31 paralogs is essential, this protein seems to function as the main L31 protein. Has a lower affinity for 70S ribosomes than the non-zinc-containing paralog L31B (ytiA); is displaced by it to varying extents, even under zinc-replete conditions.
  cofactor: Zn(2+) (Binds 1 zinc ion per subunit. This zinc stabilizes the protein.)
  subunit: Part of the 50S ribosomal subunit during exponential growth.
• The Blueprint of a Minimal Cell: MiniBacillus
  Reuß, Microbiology and molecular biology reviews : MMBR 2016
  • “...BSU01180 BSU01270 BSU27940 BSU15820 BSU01240 BSU01340 BSU37070 BSU15080 BSU24900 BSU00990 BSU41060 BSU28860 BSU01400 BSU16490 BSU01220 BSU29660 BSU01330...”

3j9wB3 / Q03223 3j9wB3 (see paper)
46% identity, 89% coverage

• Ligand: rna (3j9wB3)

RL31_THET8 / Q5SJE1 Large ribosomal subunit protein bL31; 50S ribosomal protein L31 from Thermus thermophilus (strain ATCC 27634 / DSM 579 / HB8) (see paper)
5a9zAa / Q5SJE1 of Thermous thermophilus ribosome bound to BipA-GDPCP (see paper)
48% identity, 89% coverage

• function: Binds the 23S rRNA.
  cofactor: Zn(2+) (Binds 1 zinc ion per subunit.)
  subunit: Part of the 50S ribosomal subunit.
• Ligand: rna (5a9zAa)

7msc6 / P9WHA1 70SIC in complex with MtbEttA at Pre_R0 state (see paper)
50% identity, 89% coverage

• Ligands: rna; zinc ion (7msc6)

RL31_RHOPA / Q6NBB0 Large ribosomal subunit protein bL31; 50S ribosomal protein L31; RRP-L31 from Rhodopseudomonas palustris (strain ATCC BAA-98 / CGA009) (see paper)
RPA0918 possible 50S ribosomal protein L31 from Rhodopseudomonas palustris CGA009
44% identity, 89% coverage

• function: Binds the 23S rRNA.
  subunit: Part of the 50S ribosomal subunit.
• ATP Is a Major Determinant of Phototrophic Bacterial Longevity in Growth Arrest
  Yin, mBio 2023
  • “...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, RPA3077,...”
• Characterizing the Interplay of Rubisco and Nitrogenase Enzymes in Anaerobic-Photoheterotrophically Grown Rhodopseudomonas palustris CGA009 through a Genome-Scale Metabolic and Expression Model
  Chowdhury, Microbiology spectrum 2022
  • “...change of 3-oxoacyl-acyl carrier protein reductase ( rpa3304 ) and the 50S ribosomal protein ( rpa0918 ). rpa3304 is one of the genes to convert malonyl-CoA to biotin ( 53 ). Biotin is a part of the R. palustris cell membrane ( 54 ). In Fig.2...”

5o61g / A0R215 complete structure of the Mycobacterium smegmatis 70S ribosome (see paper)
50% identity, 89% coverage

• Ligands: rna; zinc ion (5o61g)

BAB1_1728 Ribosomal protein L31 from Brucella melitensis biovar Abortus 2308
BMEI0322 LSU ribosomal protein L31P from Brucella melitensis 16M
44% identity, 93% coverage

• Proteomics-based confirmation of protein expression and correction of annotation errors in the Brucella abortus genome
  Lamontagne, BMC genomics 2010
  • “...Unknown BAB1_0418 Unknown BAB1_1230 RplQ; L17 BAB1_1693 bZIP BAB2_0243 YedY BAB1_0420 Unknown BAB1_1232 RpsK; S11 BAB1_1728 RpmE; L31 BAB2_0269 RpsU; S21 BAB1_0453 Unknown BAB1_1240 PplF; L6 BAB1_1749 Unknown BAB2_0351 OsmC-like protein BAB1_0479 RpsR, S18 BAB1_1260 RpsL; S12 BAB1_1768 Unknown BAB2_0356 Unknown BAB1_0627 Unknown BAB1_1270 SecE BAB1_1784...”
• Identification of a Novel Small Non-Coding RNA Modulating the Intracellular Survival of Brucella melitensis
  Wang, Frontiers in microbiology 2015
  • “...10 BSR1073 b AE008918 1114550-1114745 BMEII1072 BMEII1073 196 33134 11 BSR0322 b AE008917 330458-330586 BMEI0321 BMEI0322 129 2119 12 BSR0201 b AE008917 208543-208625 BMEI0200 BMEI0201 83 1577 13 BSR1915 AE008917 1969915-1970035 BMEI1914 BMEI1915 121 5112 14 BSR0742 AE008918 778863-779065 BMEII0741 BMEII0742 203 4142 15 BSR0626 b...”

cg0994 50S ribosomal protein L31 type B from Corynebacterium glutamicum ATCC 13032
Q8NS12 Large ribosomal subunit protein bL31B from Corynebacterium glutamicum (strain ATCC 13032 / DSM 20300 / JCM 1318 / BCRC 11384 / CCUG 27702 / LMG 3730 / NBRC 12168 / NCIMB 10025 / NRRL B-2784 / 534)
41% identity, 82% coverage

• Global gene expression during stringent response in Corynebacterium glutamicum in presence and absence of the rel gene encoding (p)ppGpp synthase
  Brockmann-Gretza, BMC genomics 2006
  • “...rplM 50S ribosomal protein L13 J cg0756 0.54 0.48 cstA carbon starvation protein A T cg0994 0.62 0.41 rpmE 50S ribosomal protein L31 J cg1343 0.57 0.47 narH respiratory nitrate reductase oxireductase C cg1344 0.60 0.41 narG nitrate reductase 2 ( subunit) C cg1345 0.59 0.37...”
• Heat shock response in Lactobacillus plantarum
  De, Applied and environmental microbiology 2004 (secret)

BTH_I2213 50S ribosomal protein L31 type B from Burkholderia thailandensis E264
49% identity, 84% coverage

• Gene and protein expression in response to different growth temperatures and oxygen availability in Burkholderia thailandensis
  Peano, PloS one 2014
  • “...S18 3.48 1.8 All rpsR rplI [33] BTH_I2182 ( rplI ) L9 4.92 2.3 All BTH_I2213 ( rpmE ) L31 4.92 2.3 150 All BTH_I2592 ( rplT ) L20 4.59 2.2 All rplT rpmI [33] BTH_I2593 ( rpmI ) L35 3.48 1.8 All rplT rpmI [33]...”

BPSL1491 50S ribosomal protein L31 from Burkholderia pseudomallei K96243
49% identity, 84% 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
  • “...in BPSL3261, 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...”

SMc03990 PROBABLE 50S RIBOSOMAL PROTEIN L31 from Sinorhizobium meliloti 1021
42% identity, 93% coverage

• Antimicrobial nodule-specific cysteine-rich peptides induce membrane depolarization-associated changes in the transcriptome of Sinorhizobium meliloti
  Tiricz, Applied and environmental microbiology 2013
  • “...SMc02692 SMc03770 SMc03772 SMc03859 SMc03863 SMc03881 SMc03990 SMc04003 SMc04003 SMc04320 SMc04434 (Continued on following page) 6742 aem.asm.org Applied...”
• Sinorhizobium meliloti ExoR and ExoS proteins regulate both succinoglycan and flagellum production
  Yao, Journal of bacteriology 2004
  • “...stringency control oligonucleotides directed against smc02725 and smc03990 (80% identity) were spotted in three replicates. As negative controls, 12 alien...”

ZMO1145 50S ribosomal protein L31 from Zymomonas mobilis subsp. mobilis ZM4
42% identity, 89% coverage

• Investigation of the impact of a broad range of temperatures on the physiological and transcriptional profiles of Zymomonas mobilis ZM4 for high-temperature-tolerant recombinant strain development
  Li, Biotechnology for biofuels 2021
  • “...well as ribosome protein-related genes ( ZMO0884 , ZMO0532 , ZMO1079 , ZMO0534 , and ZMO1145 ). The down-regulation of genes related to glucose metabolism at high temperature was consistent with the decrease of glucose consumption in ZM4 at high temperature (Fig. 2 ). The down-regulation...”

bglu_1g14290 Ribosomal protein L31 from Burkholderia glumae BGR1
51% identity, 77% coverage

• RNAseq-based Transcriptome Analysis of Burkholderia glumae Quorum Sensing
  Kim, The plant pathology journal 2013
  • “...0.6 1.1 0.9 bglu_1g13960 rpsR 1 0.6 1.1 1. bglu_1g13970 rplI 0.8 0.5 0.9 1.1 bglu_1g14290 rpmE2 0.8 0.6 2 1.4 bglu_1g18160 rpsU 1 1.5 0.2 0.5 bglu_1g21490 rplT 1 0.8 1.4 1.1 bglu_1g21500 rpmI 1.3 0.9 1.3 1.2 bglu_1g25990 rpsO 0.6 0.5 1.5 1.6 bglu_1g28680...”

AMUC_RS07650 type B 50S ribosomal protein L31 from Akkermansia muciniphila ATCC BAA-835
44% identity, 73% coverage

• The effect of bile acids on the growth and global gene expression profiles in Akkermansia muciniphila
  Hagi, Applied microbiology and biotechnology 2020
  • “...WP_012420121.1 AMUC_RS09135 0.692 2.57E17 gene1819 Recombinase RecQ WP_012420743.1 AMUC_RS10835 0.683 1.69E21 gene2160 Dihydrofolate reductase WP_012421055.1 AMUC_RS07650 0.661 6.98E17 gene1521 50S ribosomal protein L31 WP_035196558.1 AMUC_RS06690 0.659 3.27E15 gene1330 GDP-mannose 4%2C6-dehydratase WP_012420289.1 AMUC_RS03920 0.658 2.58E30 gene781 GTP-binding protein WP_012419774.1 AMUC_RS01615 0.655 3.21E18 gene320 Hypothetical protein WP_012419341.1 AMUC_RS01735...”

Rmet_2137 type B 50S ribosomal protein L31 from Cupriavidus metallidurans CH34
49% identity, 84% coverage

• Importance of RpoD- and Non-RpoD-Dependent Expression of Horizontally Acquired Genes in Cupriavidus metallidurans
  Große, Microbiology spectrum 2022
  • “...trxA 12.3 14 35 TGGCGCACCG 15 GCTATGATGC Rmet_2135 rho 9.1 31 35 TTGCACCTGC 13 GCCATAATCC Rmet_2137 rpmE 12.2 7 35 TTGATTCGTC 13 TCTATAATGT Rmet_2870 rpmB 14.2 38 36 TTGCCTGTCC 14 TGTATAATCG Rmet_2904 rpsT 14.4 33 35 TTGCAGTTTT 14 TTTATAATCA Rmet_3106 rplU 12.6 1,622 39 TGGCGCCGTG 15...”

P66185 Large ribosomal subunit protein bL31 from Helicobacter pylori (strain ATCC 700392 / 26695)
HP0551 ribosomal protein L31 (rpl31) from Helicobacter pylori 26695
48% identity, 89% coverage

• Outer Membrane Vesicles Secreted by Helicobacter pylori Transmitting Gastric Pathogenic Virulence Factors
  Wei, ACS omega 2022
  • “...O25257 Cag1 315 O25982 ppiA 316 O25470 HP_0781 317 O25992 HP_1453 318 O25931 TyrA 319 P66185 rpmE 320 P56162 pyrE 321 O25853 nuoD 322 P56067 cysM 323 O24884 HP_0043 324 O25510 OmpP1 325 O25421 HP_0719 326 P56075 ndk 327 P55976 nusG 328 O24991 lpxD 329 P56396...”
• 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
  • “...(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. Determination of H. pylori virulence...”
• Parallel evolution of genome structure and transcriptional landscape in the Epsilonproteobacteria
  Porcelli, BMC genomics 2013
  • “...the leadered H. pylori hp0553 ortholog. The dRNA-seq profiles for the cj0155c - cj0151c and hp0551 - hp0555 genes show that cj0153c gene has a TSS with a 70 -10 sequence, whereas hp0551 - hp0555 is transcribed as a single multicistronic mRNA, and hp0553 has a...”

C9Z0W5 Large ribosomal subunit protein bL31B from Streptomyces scabiei (strain 87.22)
SCAB_39991 putative 50S ribosomal protein L31 from Streptomyces scabiei 87.22
43% identity, 76% coverage

• The Plant Pathogenic Bacterium Streptomyces scabies Degrades the Aromatic Components of Potato Periderm via the β-Ketoadipate Pathway
  Khalil, Frontiers in microbiology 2019
  • “...release factor 2 0.07 C9ZAL3 SCAB_45881 Methyltransferase G 0.07 C9Z669 SCAB_75161 Transcription antitermination protein 0.12 C9Z0W5 SCAB_39991 50S ribosomal protein L31 type B 0.20 C9YUZ3 SCAB_36381 Transcriptional regulator 0.05 C9Z1E8 SCAB_72241 Transcriptional repressor 0.07 C9Z633 SCAB_74791 Elongation factor 0.02 Signal transduction mechanism C9Z568 SCAB_26741 Histidine kinase...”
• The Plant Pathogenic Bacterium Streptomyces scabies Degrades the Aromatic Components of Potato Periderm via the β-Ketoadipate Pathway
  Khalil, Frontiers in microbiology 2019
  • “...factor 2 0.07 C9ZAL3 SCAB_45881 Methyltransferase G 0.07 C9Z669 SCAB_75161 Transcription antitermination protein 0.12 C9Z0W5 SCAB_39991 50S ribosomal protein L31 type B 0.20 C9YUZ3 SCAB_36381 Transcriptional regulator 0.05 C9Z1E8 SCAB_72241 Transcriptional repressor 0.07 C9Z633 SCAB_74791 Elongation factor 0.02 Signal transduction mechanism C9Z568 SCAB_26741 Histidine kinase 0.01...”

FN0482 LSU ribosomal protein L31P from Fusobacterium nucleatum subsp. nucleatum ATCC 25586
42% identity, 80% coverage

• Proteomics of Fusobacterium nucleatum within a model developing oral microbial community
  Hendrickson, MicrobiologyOpen 2014
  • “...FN1287, FN1332, FN1546, FN1555, FN1556, FN1621, FN2020. 2 Covers FN0284, FN0325, FN0326, FN0329, FN0330, FN0430, FN0482, FN1117, FN1119, FN1282, FN1284, FN1285, FN1286, FN1364, FN1392, FN1437, FN1557, FN1558, FN1620, FN1623, FN1625, FN1626, FN1627, FN1628, FN1629, FN1630, FN1631, FN1632, FN1634, FN1635, FN1637, FN1638, FN1639, FN1640, FN1641, FN1642, FN1643,...”

SPO3256 50S ribosomal protein L31 from Ruegeria pomeroyi DSS-3
38% identity, 93% coverage

• A mutant fitness assay identifies bacterial interactions in a model ocean hot spot
  Schreier, Proceedings of the National Academy of Sciences of the United States of America 2023
  • “...cycle/growth 0.34 SPO1443 ATP-dependent RNA helicase RhlE ( rhlE ) Cell cycle/growth 0.44 0.36 0.42 SPO3256 ribosomal protein L31 ( rpmE ) Cell cycle/growth 3.9 SPO0691 GTP-binding protein Era ( era ) Cell cycle/growth 0.78 0.84 SPO2819 NAD(P)+ transhydrogenase, beta ( pntB ) Energy 0.39 0.36...”

EF1171 ribosomal protein L31 from Enterococcus faecalis V583
IUJ47_RS08865 type B 50S ribosomal protein L31 from Enterococcus faecalis
39% identity, 73% coverage

• Identification of proteins related to the stress response in Enterococcus faecalis V583 caused by bovine bile
  Bøhle, Proteome science 2010
  • “...protein S2 EF2398 29.5 5 24 8 2.82 1.87 0.81 31 e Ribosomal protein L31 EF1171 10.1 5.57 95 10 1.65 0.36 0.29 32 Elongation factor G EF0200 76.6 4.8 23 19 0.93 0.87 1.97 33 30S ribosomal protein S3 EF0212 24.4 9.8 12 3 0.86...”
  • “...cases an upregulation of the mRNA is not accompanied by higher protein levels (EF1499, EF2151, EF1171, EF0020, EF3184, EF3186). One may speculate that other regulatory mechanisms come into play, such as translational regulation or specific protein degradation. Two of these genes (EF3184, EF3186) are part of...”
• Characterization of the ends and target site of a novel tetracycline resistance-encoding conjugative transposon from Enterococcus faecium 664.1H1
  Roberts, Journal of bacteriology 2006
  • “...the gene encoding the ribosomal protein L31 (Cog EF1171; GenBank accession number AE016950). Interestingly, the target site for the staphylococcal SaPIbov2 is...”
• Antibacterial Components and Modes of the Methanol-Phase Extract from Commelina communis Linn
  Liu, Plants (Basel, Switzerland) 2023
  • “...ribosomal protein L28 IUJ47_RS02635 0.111 30S ribosomal protein S4 IUJ47_RS13890 0.118 30S ribosomal protein S2 IUJ47_RS08865 0.166 Type B 50S ribosomal protein L31 IUJ47_RS01035 0.166 50S ribosomal protein L11 IUJ47_RS01030 0.185 50S ribosomal protein L1 IUJ47_RS04565 0.189 50S ribosomal protein L29 IUJ47_RS04640 0.195 50S ribosomal protein...”

6o8z1 / A0A1B4XMV6 6o8z1 (see paper)
39% identity, 78% coverage

• Ligand: rna (6o8z1)

SCO1150 50S ribosomal protein L31 from Streptomyces coelicolor A3(2)
39% identity, 73% coverage

• Comparative analysis of non-coding RNAs in the antibiotic-producing Streptomyces bacteria
  Moody, BMC genomics 2013
  • “...of seven different cutoRNA pairs was significantly impacted by the loss of RNase III ( SCO1150, SCO4283, SCO4749, SCO5106, SCO5146, SCO6716, SCO6729; Additional file 1 : Table S1). cutoRNAs could also serve to tether the convergently expressed mRNAs such that their protein products are produced in...”
• Comparative genomics of Streptomyces avermitilis, Streptomyces cattleya, Streptomyces maritimus and Kitasatospora aureofaciens using a Streptomyces coelicolor microarray system
  Hsiao, Antonie van Leeuwenhoek 2008
  • “...protein 0.35 0.13 0.44 0.29 SCO0569 putative 50S ribsomomal protein fragment 0.75 0.63 0.42 0.27 SCO1150 50S ribosomal protein L31 0.56 0.47 0.24 0.14 SCO1505 30S ribosomal protein S4 0.36 0.35 0.76 0.31 SCO1598 50S ribosomal protein L20 1.50 0.63 0.89 0.34 SCO1599 50S ribosomal protein...”
• The zinc-responsive regulator Zur controls a zinc uptake system and some ribosomal proteins in Streptomyces coelicolor A3(2)
  Shin, Journal of bacteriology 2007
  • “...coelicolor genome, rpmE1 (SCO5359), rpmE2 (SCO3427), and rpmE3 (SCO1150) (6). The rpmE1 gene contains the zinc-binding motif (the gene product is C), whereas...”
  • “...motifc Proposed regulator L31 rpmE1 rpmE2 rpmE3 SCO5359 SCO3427 SCO1150 R Zur NDd L33 rpmG1 rpmG2 rpmG3 SCO4635 SCO3428 SCO0570 NDd Zur R a For the numbering...”
• Zinc-responsive regulation of alternative ribosomal protein genes in Streptomyces coelicolor involves zur and sigmaR
  Owen, Journal of bacteriology 2007
  • “...rpsR2 (SCO3425) rpmB2 (SCO3429) rpmE2 (SCO3427) rpmE3 (SCO1150) rpmF2 (SCO0436) rpmG2 (SCO3428) rpmG3 (SCO0570) rpmJ2 (SCO0569) gation from E. coli...”

MAP_RS19325 type B 50S ribosomal protein L31 from Mycobacterium avium subsp. paratuberculosis K-10
MAP3771 hypothetical protein from Mycobacterium avium subsp. paratuberculosis str. k10
34% identity, 68% coverage

• Diagnostic Sequences That Distinguish M. avium Subspecies Strains
  Bannantine, Frontiers in veterinary science 2020
  • “...WP_003873957.1 30S ribosomal protein S18 88 MAP3768c MAP_RS19310 WP_003873956.1 30S ribosomal protein S14 101 MAP3771 MAP_RS19325 WP_003873953.1 50S ribosomal protein L31 type B 97 NA MAP_RS19330 WP_003879173.1 ANTAR domain-containing protein 87 MAP3772c MAP_RS19335 WP_003873951.1 GTP-binding protein 380 MAP3774c MAP_RS19345 WP_003879175.1 Metal ABC transporter permease 285 MAP3775c...”
• Critical Role of Zur and SmtB in Zinc Homeostasis of Mycobacterium smegmatis
  Goethe, mSystems 2020
  • “...(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 protein L31 MSMEG_6071 MAP0485c (66.9) <0.0001 5.2 Metallo-beta-lactamase superfamily protein MSMEG_6211 <0.0001 4.11 Hypothetical protein MSMEG_6237 <0.0001 7.4 Class I SAM-dependent methyl-transferase MSMEG_6610 <0.0001 4.16...”
  • “...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 ribosomal protein L31 MSMEG_6071 Rv3577 (68.3) MAP0485c (66.9) <0.0001 27.95 5.20 33.42 Metallo-beta-lactamase superfamily protein MSMEG_6237 <0.0001 6.93 7.40 11.22 4.62 Class I SAM-dependent...”
• Diagnostic Sequences That Distinguish M. avium Subspecies Strains
  Bannantine, Frontiers in veterinary science 2020
  • “...MAP_RS19305 WP_003873957.1 30S ribosomal protein S18 88 MAP3768c MAP_RS19310 WP_003873956.1 30S ribosomal protein S14 101 MAP3771 MAP_RS19325 WP_003873953.1 50S ribosomal protein L31 type B 97 NA MAP_RS19330 WP_003879173.1 ANTAR domain-containing protein 87 MAP3772c MAP_RS19335 WP_003873951.1 GTP-binding protein 380 MAP3774c MAP_RS19345 WP_003879175.1 Metal ABC transporter permease 285...”
• Identification of a lineage specific zinc responsive genomic island in Mycobacterium avium ssp. paratuberculosis
  Eckelt, BMC genomics 2014
  • “...protein P - *MAP3772c - - <0.0001 140.73 cobW-like cobalamin synthesis, metal chaperone R rpmE2 MAP3771 - - <0.0001 183.4 50S ribosomal protein L31 J - *MAP3770 Rv0106 (66.1) MAV_4874 (73.5) <0.0001 218.07 cobW-like cobalamin synthesis, metal chaperone R rpmG *MAP3769c Rv2057c (85.2) MAV_4876 (93.5) <0.0001...”
• Insertion and deletion events that define the pathogen Mycobacterium avium subsp. paratuberculosis
  Alexander, Journal of bacteriology 2009
  • “...in M. intracellulare ATCC 13950T, but the ortholog of MAP3771 (rpmE2) is absent from M. avium subsp. hominissuis 104. LSPP15 (5.4 kb) contains another putative...”
• Profiling bovine antibody responses to Mycobacterium avium subsp. paratuberculosis infection by using protein arrays
  Bannantine, Infection and immunity 2008
  • “...MAP3531c MAP3734c MAP3735c MAP3743 MAP3751 MAP3753 MAP3761c MAP3771 MAP3817c MAP3833c MAP3840 MAP3902c MAP3903c MAP3954 MAP4014 MAP4025 MAP4129 MAP4198 MAP4199...”
  • “...PBS bufferg MAP2155 MAP0864 MAP0859c MAP0087-His MAP0216 MAP3771 MAP2157 MAP1416c MAP2765c MAP1643 MAP3437c MAP0852 MBP-LacZ 12.36 10.57 11.69 70.30 12.04 10.24...”
• Early antibody response against Mycobacterium avium subspecies paratuberculosis antigens in subclinical cattle
  Bannantine, Proteome science 2008
  • “...membrane protein MAP3753 0.64 1353 450 hypothetical protein MAP3761c 0.07 729 242 conserved membrane protein MAP3771 0.02 294 97 50S ribosomal protein L31 MAP3817c 0.65 939 312 no BLAST hits MAP3833c 0.13 626 208/260 hypothetical protein MAP3840 0.10 1872 623 70 kD heat shock protein, chromosome...”
  • “...0 0 18.95 15.247 A8 MAP3761c 0 2.473 14.931 23.178 0 0 18.02 21.264 G3 MAP3771 2.81 2.229 1.344 2.528 0.953 1.997 0 0 H3 MAP3817c 3.836 2.526 10.298 22.826 1.101 1.552 15.736 19.901 E9 MAP3833c 1.078 0 2.07 2.755 0 0 3.676 4.636 A4 MAP3840...”

ESA_RS12970 type B 50S ribosomal protein L31 from Cronobacter sakazakii ATCC BAA-894
38% identity, 85% coverage

• The Global Response of Cronobacter sakazakii Cells to Amino Acid Deficiency
  Chen, Frontiers in microbiology 2018
  • “...strain grown in LB medium as the control. Genes log 2 R Function BAA-894 MG1655 ESA_RS12970 ykgM 8.13 50S ribosomal protein L31 ESA_RS19300 zinT 7.68 Metal-binding protein ESA_RS03665 rbsC 6.97 ABC transporter permease ESA_RS13555 tauA 6.97 Taurine ABC transporter substrate-binding protein ESA_RS16935 thiE 6.88 Thiamine phosphate...”

lmo2548 ribosomal protein L31 from Listeria monocytogenes EGD-e
Q71WN0 Large ribosomal subunit protein bL31B from Listeria monocytogenes serotype 4b (strain F2365)
lin2692 ribosomal protein L31 from Listeria innocua Clip11262
41% identity, 80% coverage

• An Open-Source Program (Haplo-ST) for Whole-Genome Sequence Typing Shows Extensive Diversity among Listeria monocytogenes Isolates in Outdoor Environments and Poultry Processing Plants
  Louha, Applied and environmental microbiology 2020 (secret)
• Characterisation of the transcriptomes of genetically diverse Listeria monocytogenes exposed to hyperosmotic and low temperature conditions reveal global stress-adaptation mechanisms
  Durack, PloS one 2013
  • “...6.55 *** 3.90 *** 4.40 *** 3.52 *** 4.30 *** similar to uncharacterized conserved proteins lmo2548 rpmE 2.59 *** 2.49 *** 1.95 *** 3.32 ** 1.91 *** 3.69 *** ribosomal protein L31 lmo2555 1.68 *** 2.55 *** 1.15 *** 1.68 ** 1.13 *** 1.09 *** similar...”
  • “...rpsD ( lmo1596 ), rpmI ( lmo1784 ), rpmB ( lmo1816 ) and rpmE ( lmo2548 ). Although different physical stresses, both high Na + concentration and low temperature have a damaging effect on ribosome function. While high ionic concentration is thought to cause the ribosome...”
• Microarray-based characterization of the Listeria monocytogenes cold regulon in log- and stationary-phase cells
  Chan, Applied and environmental microbiology 2007
  • “...to be upregulated at 4C, including lmo1480, lmo1787, lmo2548, lmo2620, lmo2627, and lmo2856 (see Table S2 in the supplemental material). Operons encoding...”
• 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
  • “...1.036 Non-allergen 122 Q721R7 0.737 Non-allergen 123 Q71WX8 1.06 Non-allergen 124 Q71WF0 2.159 Non-allergen 125 Q71WN0 1.611 Non-allergen 126 Q725C0 0.638 Non-allergen 127 Q71ZZ5 0.527 Non-allergen 128 Q71ZG8 0.898 Non-allergen 129 Q71ZJ0 1.318 Non-allergen 130 Q71XH4 1.281 Non-allergen 131 Q71WL5 0.848 Non-allergen 132 Q720A8 0.628 Non-allergen...”
• Tetracycline resistance in Listeria monocytogenes and L. innocua from wild black bears (Ursus americanus) in the United States is mediated by novel transposable elements
  Brown, Applied and environmental microbiology 2023 (secret)

7nhn4 / P0A485 7nhn4 (see paper)
41% identity, 82% coverage

• Ligand: rna (7nhn4)

B7L427 Large ribosomal subunit protein bL31B from Escherichia coli (strain 55989 / EAEC)
36% identity, 83% coverage

• ICEEc2, a new integrative and conjugative element belonging to the pKLC102/PAGI-2 family, identified in Escherichia coli strain BEN374
  Roche, Journal of bacteriology 2010
  • “...protein Ea22 phage protein TrEMBL B4TL18 Swiss-Prot B7L427 TrEMBL Q8HAA4 Swiss-Prot P03756 Swiss-Prot P03756 Conjugative transfer Formation of type IV pilus...”

YkgM / b0296 50S ribosomal subunit protein L31B from Escherichia coli K-12 substr. MG1655 (see 8 papers)
RL31B_ECOLI / P0A7N1 Large ribosomal subunit protein bL31B; 50S ribosomal protein L31 type B from Escherichia coli (strain K12) (see 3 papers)
ECOLIN_01860 type B 50S ribosomal protein L31 from Escherichia coli Nissle 1917
NP_414830 50S ribosomal subunit protein L31B from Escherichia coli str. K-12 substr. MG1655
b0296 50S ribosomal protein L31 from Escherichia coli str. K-12 substr. MG1655
36% identity, 83% coverage

• subunit: Part of the 50S ribosomal subunit.
  disruption phenotype: Grows poorly in the absence of zinc.
• Transcriptional Profiling of the Probiotic Escherichia coli Nissle 1917 Strain under Simulated Microgravity
  Yim, International journal of molecular sciences 2020
  • “...zinT Metal ion utilization ECOLIN_02515 2.50 2.17 cytochrome o ubiquinol oxidase subunit II cyoA Uncategorized ECOLIN_01860 3.45 11.11 50 S ribosomal protein L31 type B - Uncategorized...”
• Phenotypic effects of paralogous ribosomal proteins bL31A and bL31B in E. coli.
  Lilleorg, Scientific reports 2020
  • GeneRIF: Phenotypic effects of paralogous ribosomal proteins bL31A and bL31B in E. coli.
• The Intersubunit Bridge B1b of the Bacterial Ribosome Facilitates Initiation of Protein Synthesis and Maintenance of Translational Fidelity.
  Lilleorg, Journal of molecular biology 2017 (PubMed)
  • GeneRIF: The authors conclude that the only protein-protein intersubunit bridge of the bacterial ribosome facilitates translation initiation and is essential for maintaining the reading frame of mRNA translation.
• Characterization of Zn(II)-responsive ribosomal proteins YkgM and L31 in E. coli.
  Hensley, Journal of inorganic biochemistry 2012
  • GeneRIF: Data show that maltose binding protein (MBP)-YkgM does not bind Zn(II), on the other hand, MBP-L31 tightly binds 1 equivalent of Zn(II).
• Toward Single Bacterium Proteomics
  Végvári, Journal of the American Society for Mass Spectrometry 2023
  • “...[R].LIFMLDGGDFSPPKTFSGK.[L] 2744.53 915.51 +3 85.46 1 219.47 6.25% 50S ribomal protein L31 type B ykgM P0A7N1 [1130] [R].TVVFHDTSVDEYFKIGSTIK.[T] 2744.49 686.88 +4 85.49 1 194.53 6.25% tRNA (guanine-N(1)-)-methyltransferase trmD P0A873 [6975] [R].DAIHAAK.[A] 1183.72 395.25 +3 31.52 2 214.27 12.50% ATP-dependent RNA helicase HrpA hrpA P43329 [988993] [R].SLQDLK.[D]...”
• FLASHIda enables intelligent data acquisition for top-down proteomics to boost proteoform identification counts
  Jeong, Nature communications 2022
  • “...(UniProtKB: P02413) were reported, 34 proteoform IDs of 50S ribosomal protein L31 type B (UniProtKB: P0A7N1) were identified in a single FI90 dataset. The relative intensities of the ribosomal proteoform IDs from the same protein were also often two orders of magnitude apart (e.g., UniProtKB: P0A7N1,...”
  • “...datasets from top four selected proteins (two ribosomal proteins and two binding proteins; UniProtKB: P0ACF8, P0A7N1, P76344, P60438) with the four highest proteoform ID diversity. It also provides the manual validation results and possible interpretations for the modifications (see also Supplementary Figs. 23 27 for example...”
• The Escherichia coli proteome: past, present, and future prospects
  Han, Microbiology and molecular biology reviews : MMBR 2006
  • “...ribosomal protein L25 9.60/10,693.44 10.61/11,560 (6-11) RpmE2 P0A7N1 50S ribosomal protein L31 type B 9.30/9,920.20 8.30/9,673 (6-11) RpoA P0A7Z4 DNA-directed...”
• Severe zinc depletion of Escherichia coli: roles for high affinity zinc binding by ZinT, zinc transport and zinc-independent proteins
  Graham, The Journal of biological chemistry 2009
  • “...2.88 2.86 2.86 0.00117 0.00386 0.00998 ykgM mdtD b0296 b2077 2.64 2.46 0.03647 0.01614 ribA ydfE aslA b1277 b1577 b3801 Periplasmic cadmium-binding protein;...”
• Effect of an artificial RNA marker on gene expression in Escherichia coli
  Tucker, Applied and environmental microbiology 2005
  • “...2.958 2.499 deoC b4381 0.018262 2.025 ykgM tmk b0296 b1098 0.037316 0.049627 1.625 1.625 deoB b4383 0.048425 deoD b4384 ribH chpR M9 minimal medium-expressed...”
• Definition of the Escherichia coli MC4100 genome by use of a DNA array
  Peters, Journal of bacteriology 2003
  • “...fruB,a lacY yeiO, ykgG, b0263 b0288, b0328, fruKa mcrAa b0296 betA, betB, betI, ykgC codA argF, yagF cynR, lacA, lacI, lacZ, mhpB, yagG, yeiQ, b0271, b0349...”

F452_RS0105140 type B 50S ribosomal protein L31 from Porphyromonas gulae DSM 15663
PGN_0636 50S ribosomal protein L31 from Porphyromonas gingivalis ATCC 33277
PG0592 ribosomal protein L31 from Porphyromonas gingivalis W83
41% identity, 76% coverage

• Antibacterial effects of sodium tripolyphosphate against Porphyromonas species associated with periodontitis of companion animals
  Lee, Journal of veterinary science 2019
  • “...Differentially expressed genes related to ribosome Locus name Functional annotation Adjusted p value Fold change F452_RS0105140 50S ribosomal protein L31 type B 3.73E-66 +9.92 F452_RS0105705 50S ribosomal protein L19 3.37E-64 +8.81 F452_RS0100530 30S ribosomal protein S21 1.88E-100 +10.72 F452_RS0103275 30S ribosomal protein S20 2.71E-63 +10.28 F452_RS0100215...”
• Synthesis of ppGpp impacts type IX secretion and biofilm matrix formation in Porphyromonas gingivalis
  Kim, NPJ biofilms and microbiomes 2020
  • “...2.07 PGN_0394 rpsT 30S ribosomal protein S20 2.39 PGN_0426 rpsC 30S ribosomal protein S3 3.20 PGN_0636 rpmE2 50S ribosomal protein L31 4.02 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...”
• Pathway analysis for intracellular Porphyromonas gingivalis using a strain ATCC 33277 specific database
  Hendrickson, BMC microbiology 2009
  • “...(32) Unchanged (19) Decreased Levels (1) PGN_0035 PGN_0167 PGN_0640 PGN_0965 PGN_0394 PGN_0188 PGN_0279 PGN_1572 PGN_1589 PGN_0636 PGN_0639 PGN_1647 PGN_1648 PGN_0641 PGN_0964 PGN_1698 PGN_1844 PGN_1088 PGN_1219 PGN_1651 PGN_1852 PGN_1573 PGN_1575 PGN_1853 PGN_1854 PGN_1588 PGN_1590 PGN_1855 PGN_1861 PGN_1832 PGN_1840 PGN_1863 PGN_1868 PGN_1842 PGN_1843 PGN_1872 PGN_1890 PGN_1849 PGN_1850 PGN_1891...”
• Microarray analysis of the transcriptional responses of Porphyromonas gingivalis to polyphosphate
  Moon, BMC microbiology 2014
  • “...Ribosomal protein L21 1.90 PG0315 50S 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...”
• VimA-dependent modulation of the secretome in Porphyromonas gingivalis
  Osbourne, Molecular oral microbiology 2012
  • “...biosynthesis 120 kDa 3 0 Hypothetical protein PG0552 Unknown 37 kDa 10 0 Hypothetical protein PG0592 Unknown 45 kDa 29 0 Heme-binding protein/peripheral outer membrane chelatase PG0602 Cell envelope 33 kDa 10 0 Outer membrane protein PG0626 Cell envelope 42 kDa 10 0 TonB-dependent receptor HmuY...”
  • “...3 0 Hypothetical protein PG0552 Unknown C No No 37 kDa 10 0 Hypothetical protein PG0592 Unknown OM Yes Yes 45 kDa 29 0 Heme-binding protein/peripheral outer membrane chelatase PG0602 Cell envelope PERI Yes Partial 33 kDa 10 0 Outer membrane protein PG0626 Cell envelope OM...”

6ysiW / D0CBZ8 Acinetobacter baumannii ribosome-tigecycline complex - 50s subunit (see paper)
56% identity, 58% coverage

• Ligand: rna (6ysiW)

SMU_1298 type B 50S ribosomal protein L31 from Streptococcus mutans UA159
37% identity, 81% coverage

• Protein Interactomes of Streptococcus mutans YidC1 and YidC2 Membrane Protein Insertases Suggest SRP Pathway-Independent- and -Dependent Functions, Respectively
  Lara, mSphere 2021
  • “...and protein a Translation 50S ribosomal protein L14 (SMU_2017) 50S ribosomal protein L31 type B (SMU_1298) 50S ribosomal protein L16 (SMU_2020) tRNA uridine 5-carboxymethylaminomethyl modification protein (SMU_2141) Translocation Preprotein translocase subunit SecA (SMU_1838) Preprotein translocase subunit YajC (SMU_1787c) DNA replication/repair DNA-directed RNA polymerase subunit beta' (SMU_1989)...”

PMT1760 50S ribosomal protein L31 from Prochlorococcus marinus str. MIT 9313
42% identity, 77% coverage

• Operon prediction by comparative genomics: an application to the Synechococcus sp. WH8102 genome
  Chen, Nucleic acids research 2004
  • “...PMM1530 PMM1529 PMM1049 PMT1467 PMT1466 PMT1758 PMT1759 PMT1760 PMT1761 PMT1145 SYNW0708 PMM1048 PMT1146 SYNW1341 PMM0601 PMT0418 9 SYNW1340 SYNW1090 SYNW1091...”

PD0749 50S ribosomal protein L31 from Xylella fastidiosa Temecula1
38% identity, 81% coverage

• Characterization of regulatory pathways in Xylella fastidiosa: genes and phenotypes controlled by algU
  Shi, Applied and environmental microbiology 2007
  • “...PD0445 PD0447 PD0450 PD0451 PD0452 PD0454 PD0455 PD0458 PD0488 PD0489 PD0749 50S 50S 50S 50S 50S 30S 30S 50S 30S 50S 30S 50S 50S 50S 0.449 0.499 0.426 0.479...”

PMM1530 50S ribosomal protein L31 from Prochlorococcus marinus sp. MED4
42% identity, 79% coverage

• Operon prediction by comparative genomics: an application to the Synechococcus sp. WH8102 genome
  Chen, Nucleic acids research 2004
  • “...SYNW2095 SYNW2096 SYNW0709 PMM1451 PMM1450 PMM1532 PMM1531 PMM1530 PMM1529 PMM1049 PMT1467 PMT1466 PMT1758 PMT1759 PMT1760 PMT1761 PMT1145 SYNW0708 PMM1048...”

SSA_1272 50S ribosomal protein L31 type B, putative from Streptococcus sanguinis SK36
36% identity, 81% coverage

• Availability of Zinc Impacts Interactions between Streptococcus sanguinis and Pseudomonas aeruginosa in Coculture
  Li, Journal of bacteriology 2020 (secret)

gbs0581 50S ribosomal protein L31 from Streptococcus agalactiae NEM316
36% identity, 76% coverage

• The novel fibrinogen-binding protein FbsB promotes Streptococcus agalactiae invasion into epithelial cells
  Gutekunst, Infection and immunity 2004
  • “...FbsB protein, and to the N terminus of the Gbs0581 fusion protein. The fusion proteins FbsB and Gbs0851 were synthesized in E. coli BL21 and subsequently...”

MHO_3020 50S ribosomal protein L31 from Mycoplasma hominis
43% identity, 82% coverage

• Genome-wide Analysis of Mycoplasma hominis for the Identification of Putative Therapeutic Targets
  Parvege, Drug target insights 2014
  • “...Novel 54 MHO_2900 50S ribosomal protein L29 Cytoplasm 0 No (79) 50 No Novel 55 MHO_3020 50S ribosomal protein L31 Cytoplasm 0 No (78) 50 No Novel 56 MHO_3920 50S ribosomal protein L9 Cytoplasm 0 No (71) 50 No Novel 57 MHO_0630 Carbamate kinase Cytoplasm 0...”

SCO3427 50S ribosomal protein L31 from Streptomyces coelicolor A3(2)
38% identity, 77% coverage

• Comparative genomics of Streptomyces avermitilis, Streptomyces cattleya, Streptomyces maritimus and Kitasatospora aureofaciens using a Streptomyces coelicolor microarray system
  Hsiao, Antonie van Leeuwenhoek 2008
  • “...protein L21 0.27 0.08 0.64 0.18 SCO3124 ribosomal L25p family protein 0.39 0.31 0.23 0.89 SCO3427 putative 50S ribosomal protein 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...”
• The zinc-responsive regulator Zur controls a zinc uptake system and some ribosomal proteins in Streptomyces coelicolor A3(2)
  Shin, Journal of bacteriology 2007
  • “...in the S. coelicolor genome, rpmE1 (SCO5359), rpmE2 (SCO3427), and rpmE3 (SCO1150) (6). The rpmE1 gene contains the zinc-binding motif (the gene product is...”
  • “...Cysteine motifc Proposed regulator L31 rpmE1 rpmE2 rpmE3 SCO5359 SCO3427 SCO1150 R Zur NDd L33 rpmG1 rpmG2 rpmG3 SCO4635 SCO3428 SCO0570 NDd Zur R a For the...”
• Zinc-responsive regulation of alternative ribosomal protein genes in Streptomyces coelicolor involves zur and sigmaR
  Owen, Journal of bacteriology 2007
  • “...rpsN2 (SCO3430) rpsR2 (SCO3425) rpmB2 (SCO3429) rpmE2 (SCO3427) rpmE3 (SCO1150) rpmF2 (SCO0436) rpmG2 (SCO3428) rpmG3 (SCO0570) rpmJ2 (SCO0569) gation from E....”

SPD_1154 ribosomal protein L31 from Streptococcus pneumoniae D39
SP_1299 50S ribosomal protein L31 type B from Streptococcus pneumoniae TIGR4
36% identity, 81% coverage

• Two DHH subfamily 1 proteins in Streptococcus pneumoniae possess cyclic di-AMP phosphodiesterase activity and affect bacterial growth and virulence
  Bai, Journal of bacteriology 2013
  • “...5A), and pde2 may also be in an operon with SPD_1154 (Fig. 5B). Deletion of either pde1 or pde2 simply by replacement with a drug resistance marker may result...”
• Genome-wide identification of Streptococcus pneumoniae genes essential for bacterial replication during experimental meningitis
  Molzen, Infection and immunity 2011
  • “...protease, proteolytic subunit 1.2ns 2.3 5.1 Protein synthesis SP_1299 SP_2206 rpmE yfiA Ribosomal protein L31 Ribosomal subunit interface protein 2.8 2.8 10.0...”
  • “...protein, and cardiolipin synthetase; and SP_1296 to SP_1299, encoding a putative chorismate mutase, flavodoxin, a DHH subfamily protein of unknown function,...”
• A variable region within the genome of Streptococcus pneumoniae contributes to strain-strain variation in virulence
  Harvey, PloS one 2011
  • “...in P1031. This region is inserted between homologues of SPINV104_11210 and 11240 in INV104 and SP_1299 and 1306 in TIGR4. In both TIGR4 and INV104 the corresponding region consists of a number of small hypothetical genes. Whilst the substrate of the permease in region 6 requires...”

STM0469 putative 50S ribosomal protein L31 (second copy) from Salmonella typhimurium LT2
SEN0450 putative 50s ribosomal protein L31 (second copy) from Salmonella enterica subsp. enterica serovar Enteritidis str. P125109
JJB80_02375 type B 50S ribosomal protein L31 from Salmonella enterica subsp. enterica serovar Typhimurium
34% identity, 84% coverage

• Quantitative mass spectrometry catalogues Salmonella pathogenicity island-2 effectors and identifies their cognate host binding partners
  Auweter, The Journal of biological chemistry 2011
  • “...ratio of >2 ID a b PSLT037 PSLT038 STM0469 STM0972 STM1224 STM1398 STM1400 STM1401 STM1631 STM1698 STM1583 STM1540 STM2817 STM2444 STM2287 STM2780 STM1263...”
• Global transcriptomic analysis of ethanol tolerance response in Salmonella Enteritidis
  He, Current research in food science 2022
  • “...L33 SEN3246 rpsM 3.41 30S ribosomal protein S13 SEN3259 rpsQ 4.77 30S ribosomal protein S17 SEN0450 rpmE2 5.27 50S ribosomal protein L31 SEN3137 rplU 2.89 50S ribosomal protein L21 SEN3269 rpsJ 3.67 30S ribosomal subunit protein S10 SEN3245 rpsK 3.34 30S ribosomal protein S11 SEN3177 rpsL...”
• Reassembling a cannon in the DNA defense arsenal: Genetics of StySA, a BREX phage exclusion system in Salmonella lab strains
  Zaworski, PLoS genetics 2022
  • “...Of the 37 genes increased in R + M + strain J, 1 is unique: JJB80_02375, a ribosomal protein associated with changes in frameshifting. It seems unlikely that these extra-locus changes are responsible for the M and R phenotypes. A very striking result is that strains...”

LLNZ_04655 type B 50S ribosomal protein L31 from Lactococcus cremoris subsp. cremoris NZ9000
35% identity, 80% coverage

• Genomics and transcriptomics analysis reveals the mechanism of isobutanol tolerance of a laboratory evolved Lactococcus lactis strain
  Gupta, Scientific reports 2020
  • “...Table 5 Maximally downregulated genes in 4B0 culture. S. No Locus_tag Annotation KEGG pathway 1 LLNZ_04655 50S ribosomal protein L31 type B Translation 2 LLNZ_13115 Glyceraldehyde 3-phosphate dehydrogenase Glycolysis/gluconeogenesis 3 LLNZ_08605 50S ribosomal protein L19 Translation 4 LLNZ_09890 30S ribosomal protein S20 Translation 5 LLNZ_08905 30S...”

5myjB3 / A2RJP7 of 70S ribosome from Lactococcus lactis (see paper)
35% identity, 82% coverage

• Ligand: rna (5myjB3)

ssl3445 50S ribosomal protein L31 from Synechocystis sp. PCC 6803
42% identity, 79% coverage

• Proteomic and metabolomic analyses reveal metabolic responses to 3-hydroxypropionic acid synthesized internally in cyanobacterium Synechocystis sp. PCC 6803
  Wang, Biotechnology for biofuels 2016
  • “...in strain SM when 3-HP was produced. Eight proteins ( i.e. , Sll1746, Sll1807, Slr1678, Ssl3445, Ssr1398, Ssl1784, Ssl2233 and Ssr1399) involved in ribosome synthesis were also up-regulated. Sll1746, Sll1807, Slr1678, Ssl3445 and Ssr1398 were annotated as 50S ribosomal protein subunits and Ssl1784, Ssl2233 and Ssr1399...”
• A transcriptional regulator Sll0794 regulates tolerance to biofuel ethanol in photosynthetic Synechocystis sp. PCC 6803
  Song, Molecular & cellular proteomics : MCP 2014
  • “...Slr2041 Slr2059 Ssl1426 Ssl1784 Ssl3044 Ssl3432 Ssl3441 Ssl3445 Ssr0482 Ssr1604 Ssr2799 Mutant_r1 vs. Control_r1 Mutant_r2 vs. Control_r1 Mutant_r1 vs....”
• Gene expression patterns of sulfur starvation in Synechocystis sp. PCC 6803
  Zhang, BMC genomics 2008
  • “...), Ribosomal proteins (sll1816( rps13 ), slr1984( rps1 ), sml0006( rpl36 ), ssl3437( rps17 ), ssl3445( rpl31 ), ssr0482( rps16 )) 20 slr2075( groES ), Ribosomal proteins (sll1824, slr0628( rps14 ), ssl2233( rps20 )) The differentially expressed genes in Synechocystis sulfate deprivation time course were identified...”
• Global gene expression profiles of the cyanobacterium Synechocystis sp. strain PCC 6803 in response to irradiation with UV-B and white light
  Huang, Journal of bacteriology 2002
  • “...sll1813 sll1805 sll1819 sll1811 sll1803 sll1801 sll1807 ssl3436 ssl3445 sll1804 sll1812 sll1809 sll1822 sll1101 ssl3437 ssl3432 0.76 0.14 0.7 0.3 0.99 0.18 0.51...”

VC0878 ribosomal protein, L31P family from Vibrio cholerae O1 biovar eltor str. N16961
35% identity, 85% coverage

• Transcriptomics reveals a cross-modulatory effect between riboflavin and iron and outlines responses to riboflavin biosynthesis and uptake in Vibrio cholerae
  Sepúlveda-Cisternas, Scientific reports 2018
  • “...VC0855 dnaK dnaK protein 1.560 VC0856 dnaJ dnaJ protein 1.504 VC0863 conserved hypothetical protein 1.115 VC0878 rpmE2 ribosomal protein L31P family 1.276 VC0879 rpmJ ribosomal protein L36 putative 1.121 VC0895 hypothetical protein 1.190 VC0905 metQ D-methionine transport system substrate-binding protein 1.230 VC1049 aphB transcriptional regulator LysR...”
• Mapping the regulon of Vibrio cholerae ferric uptake regulator expands its known network of gene regulation
  Davies, Proceedings of the National Academy of Sciences of the United States of America 2011
  • “...site upstream of an alternative ribosomal protein, VC0878, that showed 300fold enrichment. Table 1. Known vcFur-regulated genes associated with vcFur ChIP-peaks...”
  • “...VC0914 VC1235 VC2012 VC2334 VCA0355 VCA1098 VC0878 VC0534 VC2080 Intergenic VC0142/VC0143 Intergenic VCA0452/VCA0453 VC2190 (flgL) VCA1091 (cheR-3) VC0019...”
• Comparative genomics of bacterial zinc regulons: enhanced ion transport, pathogenesis, and rearrangement of ribosomal proteins
  Panina, Proceedings of the National Academy of Sciences of the United States of America 2003
  • “...its orthologs in ST (rpmE2), YP (YP03134), and VC (VC0878). This gene encodes a paralog of the ribosomal protein L31 (see below). To identify candidate...”

VP_RS11315 type B 50S ribosomal protein L31 from Vibrio parahaemolyticus RIMD 2210633
VP2331 ribosomal protein, L31P family from Vibrio parahaemolyticus RIMD 2210633
38% identity, 84% coverage

• ZrgA contributes to zinc acquisition in Vibrio parahaemolyticus
  Zheng, Virulence 2023
  • “...VP_RS09335 2.1031618 ribA GTP cyclohydrolase II VP_RS11310 648.4014599 rpmJ2 type B 50S ribosomal protein L36 VP_RS11315 656.141252 rpmE2 type B 50S ribosomal protein L31 VP_RS21420 283.3969466 znuBII metal ABC transporter permease VP_RS21425 543.025974 znuAII zinc ABC transporter substrate-binding protein VP_RS21430 1033.615741 omr Zinc-regulated TonB-dependent outer membrane...”
• Rapid identification of Vibrio parahaemolyticus by whole-cell matrix-assisted laser desorption ionization-time of flight mass spectrometry
  Hazen, Applied and environmental microbiology 2009
  • “...0 0 VP3074 VP2780 VP0098 Predicted protein VP2817 VP2331 VP2582 VP0160 VP1210 VP0261 VP1294 VP1283 VP0268 VPA1222 VP2986 VP2923 VP2766 VP2178 VP0262 VP0280...”
  • “...ribosomal protein L17 VP0275 VP2529 VP0265 VP2335 VP2817 VP2331 VP0160 VP1210 VP0261 VPA0321 VPA0286 VP2627 VP2619 VP2029 VPA0577 VP2530 VP0646 VP0448 VP0283...”

SYNW2095 50S ribosomal protein L31 from Synechococcus sp. WH 8102
43% identity, 74% coverage

• Operon prediction by comparative genomics: an application to the Synechococcus sp. WH8102 genome
  Chen, Nucleic acids research 2004
  • “...PMT1469 PMT1468 2.72 SYNW0494 SYNW0495 SYNW2093 SYNW2094 SYNW2095 SYNW2096 SYNW0709 PMM1451 PMM1450 PMM1532 PMM1531 PMM1530 PMM1529 PMM1049 PMT1467 PMT1466...”

E2P69_RS10215, XAC29_17265 type B 50S ribosomal protein L31 from Xanthomonas axonopodis Xac29-1
35% identity, 81% coverage

• Transcriptome profiling of type VI secretion system core gene tssM mutant of Xanthomonas perforans highlights regulators controlling diverse functions ranging from virulence to metabolism
  Ramamoorthy, Microbiology spectrum 2024
  • “...that have evolved to combat environmental stress. For example, the transcript abundance of two genes (E2P69_RS10215 and E2P69_RS08540) coding for type B 50S ribosomal protein L31 and L36 was significantly higher in the mutant strain at 8 and 16 hours. These genes play a vital role...”
• Biological and transcriptomic studies reveal hfq is required for swimming, biofilm formation and stress response in Xanthomonas axonpodis pv. citri
  Liu, BMC microbiology 2019
  • “...the reliability of RNA-seq analysis. The down-regulation expression of XAC29_11660 (50S ribosomal protein L36) and XAC29_17265 (50S ribosomal protein L31) by RT-qPCR was inconsistent with those obtained from the RNA-seq. Fig. 5 RT-qPCR of 26 selected differentially expressed genes (DEGs) related with bacterial chemotaxis ( a...”

U876_13185 type B 50S ribosomal protein L31 from Aeromonas hydrophila NJ-35
36% identity, 82% coverage

• Comparative transcriptomic and proteomic analyses reveal upregulated expression of virulence and iron transport factors of Aeromonas hydrophila under iron limitation
  Teng, BMC microbiology 2018
  • “...metabolism|Carbon fixation pathways in prokaryotes 2.3607 U876_16675 Quorum sensing 2.3034 U876_14615 Oxidative phosphorylation|Two-component system 2.1593 U876_13185 Ribosome 1.7769 U876_13000 Cysteine and methionine metabolism|Selenocompound metabolism 1.5614 U876_17160 RNA transport 1.4601 U876_00445 Glycine, serine and threonine metabolism 1.5113 U876_10020 Purine metabolism|Drug metabolism - other enzymes 1.5726 U876_15390 Biotin...”

STER_0787, STER_RS03860 type B 50S ribosomal protein L31 from Streptococcus thermophilus
35% identity, 81% coverage

• Streptococcus thermophilus: A Source of Postbiotics Displaying Anti-Inflammatory Effects in THP 1 Macrophages
  Allouche, Molecules (Basel, Switzerland) 2024
  • “...peptides, i.e., 78 and 126 for LMD-9 and CNRZ-21N strains, respectively. The putative ribosomal protein (STER_0787) and the 50S ribosomal protein L18 (STER_1891) were only identified in IPH from LMD-9 strain and generated 15 and 11 sequences, respectively. In contrast, the ribosomal protein S21 and L31...”
• Identification of Hanks-Type Kinase PknB-Specific Targets in the Streptococcus thermophilus Phosphoproteome
  Henry, Frontiers in microbiology 2019
  • “...protein S1 YP_820100.1 WP_011680912.1 STER_0639 STER_RS03135 RpmE 50S Ribosomal protein L31 type B YP_820233.1 WP_002945948.1 STER_0787 STER_RS03860 PrfA Peptide chain release factor A YP_820239.1 WP_002948472.1 STER_0793 STER_RS03890 QueF NADPH-dependent 7-cyano-7-deazaquanine reductase YP_820305.1 WP_002946191.1 STER_ 0872 STER_RS04310 RpmC 50S Ribosomal protein L29 YP_821209.1 WP_002952156.1 STER_1899 STER_RS09305 Fus...”
  • “...S1 YP_820100.1 WP_011680912.1 STER_0639 STER_RS03135 RpmE 50S Ribosomal protein L31 type B YP_820233.1 WP_002945948.1 STER_0787 STER_RS03860 PrfA Peptide chain release factor A YP_820239.1 WP_002948472.1 STER_0793 STER_RS03890 QueF NADPH-dependent 7-cyano-7-deazaquanine reductase YP_820305.1 WP_002946191.1 STER_ 0872 STER_RS04310 RpmC 50S Ribosomal protein L29 YP_821209.1 WP_002952156.1 STER_1899 STER_RS09305 Fus Elongation...”

MPN360 ribosomal protein L31 from Mycoplasma pneumoniae M129
40% identity, 68% coverage

• Quantitative essentiality in a reduced genome: a functional, regulatory and structural fitness map
  Miravet-Verde, 2025

B7C60_RS12925 type B 50S ribosomal protein L31 from Vibrio fujianensis
38% identity, 83% coverage

• Comparative Genomics and Transcriptomics Analyses Reveal a Unique Environmental Adaptability of Vibrio fujianensis
  Huang, Microorganisms 2020
  • “...rpmA large subunit ribosomal protein L27 Translation B7C60_RS11455 rpsU small subunit ribosomal protein S21 Translation B7C60_RS12925 rpmE large subunit ribosomal protein L31 Translation Downregulated B7C60_RS00940 rplI large subunit ribosomal protein L9 Translation B7C60_RS00945 rpsR small subunit ribosomal protein S18 Translation B7C60_RS00950 rpsF small subunit ribosomal protein...”

RL31_DEIRA / Q9RW44 Large ribosomal subunit protein bL31; 50S ribosomal protein L31 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)
1nkwY / Q9RW44 Crystal structure of the large ribosomal subunit from deinococcus radiodurans (see paper)
40% identity, 89% coverage

• function: Binds the 23S rRNA and interacts with the tRNA in the E site
  subunit: Part of the 50S ribosomal subunit. Contacts protein L9.
• Ligand: rna (1nkwY)

LSEI_2569 Ribosomal protein L31 from Lactobacillus casei ATCC 334
38% identity, 78% coverage

• Physiological and transcriptional response of Lactobacillus casei ATCC 334 to acid stress
  Broadbent, Journal of bacteriology 2010
  • “...LSEI_1579 LSEI_1280 LSEI_1485 LSEI_1703 LSEI_0883 LSEI_2569 LSEI_1697 LSEI_1642 LSEI_1641 LSEI_1640 LSEI_1644 LSEI_1645 LSEI_1847 LSEI_1572 LSEI_1573 LSEI_1574...”

Psyr_3920 Ribosomal protein L31 from Pseudomonas syringae pv. syringae B728a
33% identity, 77% coverage

• Core regulon of the global anaerobic regulator Anr targets central metabolism functions in Pseudomonas species
  Tribelli, Scientific reports 2019
  • “...capB , dcd and PP1135 and only 1 for P. syringae B728a located upstream of Psyr_3920 ( rpmE2 ) (Fig. 2A ). No unique Anr-boxes were found for P. protegens Pf-5. When non-pathogenic model species ( P. extremaustralis 14-3b, P. protegens Pf-5 and P. putida KT2440)...”

BAS5180 ribosomal protein L31 from Bacillus anthracis str. Sterne
BA5574 ribosomal protein L31 from Bacillus anthracis str. Ames
35% identity, 80% coverage

• Identification of a protein subset of the anthrax spore immunome in humans immunized with the anthrax vaccine adsorbed preparation
  Kudva, Infection and immunity 2005
  • “...of aspartate family BAS3739 BAS4303 BAS5179 BAS5180 BAS0286 BA4027 BA4638 BA5573 BA5574 BA0299 pyrC/PyrC; dihydroorotase/pyrimidine ribonucleotide biosynthesis...”
• Identification of a protein subset of the anthrax spore immunome in humans immunized with the anthrax vaccine adsorbed preparation
  Kudva, Infection and immunity 2005
  • “...BAS0286 BA4027 BA4638 BA5573 BA5574 BA0299 pyrC/PyrC; dihydroorotase/pyrimidine ribonucleotide biosynthesis apt/Apt; adenine phosphoribosyltransferase/salvage...”

7nhl4 / Q2FWD8 7nhl4 (see paper)
41% identity, 82% coverage

• Ligand: rna (7nhl4)

SERP1727 ribosomal protein L31 from Staphylococcus epidermidis RP62A
35% identity, 76% coverage

• Concentration-Dependent Global Quantitative Proteome Response of Staphylococcus epidermidis RP62A Biofilms to Subinhibitory Tigecycline
  Sung, Cells 2022
  • “...H Nicotinate phosphoribosyltransferase 0.00 0.00 1000.00 SERP0168 gltX fig|176279.9.peg.159 J Glutamate--tRNA ligase 1000.00 1000.00 4.77 SERP1727 rpmE2 fig|176279.9.peg.1686 J 50S ribosomal protein L31 type B 1.19 1.44 1.52 SERP0179 rplA fig|176279.9.peg.170 J 50S ribosomal protein L1 2.54 10.12 12.84 SERP1743 deoB fig|176279.9.peg.1702 G Phosphopentomutase 19.11 4.55...”

5li03 / Q2FWD8 5li03 (see paper)
37% identity, 78% coverage

• Ligand: rna (5li03)

SA1922 ribosomal protein L31 from Staphylococcus aureus subsp. aureus N315
Q2FF08 Large ribosomal subunit protein bL31B from Staphylococcus aureus (strain USA300)
Q2FWD8 Large ribosomal subunit protein bL31B from Staphylococcus aureus (strain NCTC 8325 / PS 47)
Q6GEV5 Large ribosomal subunit protein bL31B from Staphylococcus aureus (strain MRSA252)
37% identity, 77% coverage

• Transcriptional profiles of the response of methicillin-resistant Staphylococcus aureus to pentacyclic triterpenoids
  Chung, PloS one 2013
  • “...rplC 50S ribosomal protein L3 4.9 Translation SA2030 rpmD 50S ribosomal protein L30 6.2 Translation SA1922 rpmE 50S ribosomal protein L31 type B 4.8 Translation SAS033 rpmF 50S ribosomal protein L32 7.7 Translation SAS042 rpmG 50S ribosomal protein L33 1,2,3 8.4 Translation SAS093 rpmH 50S ribosomal...”
• The Spl Serine Proteases Modulate Staphylococcus aureus Protein Production and Virulence in a Rabbit Model of Pneumonia
  Paharik, mSphere 2016
  • “...0.01 Q2FFJ6 ( GATB_STAA3 ) Aspartyl/glutamyl-tRNA(Asn/Gln) amidotransferase subunit B GatB Housekeeping, translation 0.00 6.00 0.0002 Q2FF08 ( RL31B_STAA3 ) 50S ribosomal protein L31 type B RpmE2 Housekeeping, translation 2.67 7.00 0.0096 Q2FEQ7 ( RL30_STAA3 ) 50S ribosomal protein L30 RpmD Housekeeping, translation 0.00 2.33 0.007 Q2FJU4...”
• Antimicrobial Activity and Mechanism of Action of Dracocephalum moldavica L. Extracts Against Clinical Isolates of Staphylococcus aureus
  Yu, Frontiers in microbiology 2019
  • “...3.53 0.002208 Q2G2M7 Serine acetyltransferase CysE 3.39 0.007534 Q2G0B7 Lysine decarboxylase family YvdD 3.12 0.000743 Q2FWD8 50S ribosomal L31 type B RpmE 3.01 0.001282 Q2G1D8 Formate acetyltransferase PflB 2.88 0.00 Q2G0Q0 Pyridoxine biosynthesis amidotransferase PdxT 2.73 0.000367 Q2FYK6 Dihydrofolate reductase FolA 2.47 0.00 Q2FVL9 Nitrite reductase...”
• Structural and Functional Dynamics of Staphylococcus aureus Biofilms and Biofilm Matrix Proteins on Different Clinical Materials
  Hiltunen, Microorganisms 2019
  • “...Q6GEJ1 50S ribosomal protein L3 Q6GEI3 50S ribosomal protein L30 Q6GEK1 50S ribosomal protein L31 Q6GEV5 50S ribosomal protein L35 Q6GG26 50S ribosomal protein L4 Q6GEI4 50S ribosomal protein L5 Q99S33 50S ribosomal protein L6 Q99S36 50S ribosomal protein L7/L12 Q6GJC8 50S ribosomal protein L9 Q6GKT0...”

BB0229 ribosomal protein L31 (rpmE) from Borrelia burgdorferi B31
33% identity, 79% coverage

• The In Vitro Antimicrobial Susceptibility of Borrelia burgdorferi sensu lato: Shedding Light on the Known Unknowns
  Hunfeld, Pathogens (Basel, Switzerland) 2023
  • “...d 26.569 Pfs protein (Pfs-1) (BB0375) D-0504 5.2 42 d 42.372 Cell division protein (FtsZ) (BB0229) D-4101 6.4 26 u 27.984 Triosephosphate isomerase Proteins were identified by MALDI-TOF MS after preparative isolation from 2-DE gels. p I: isoelectric point; P: proteins affected by penicillin G exposure;...”
• Correction: Characterization of the RelBbu regulon in Borrelia burgdorferi reveals modulation of glycerol metabolism by (p)ppGpp
  PLOS, PloS one 2015
  • “...1.03 0.004 1.95 <0.001 BB0789 cell division protein ( ftsH ) 1.01 <0.001 Protein synthesis BB0229 ribosomal protein L31 ( rpmE ) 1.54 <0.001 BB0251 leucyl-tRNA synthetase ( leuS ) 3.41 <0.001 BB0514 phenylalanyl-tRNA synthetase, subunit ( pheT ) 1.63 0.009 BB0615 ribosomal protein S4 (...”
• Characterization of the RelBbu Regulon in Borrelia burgdorferi Reveals Modulation of Glycerol Metabolism by (p)ppGpp
  Bugrysheva, PloS one 2015
  • “...1.03 0.004 1.95 <0.001 BB0789 cell division protein ( ftsH ) 1.01 <0.001 Protein synthesis BB0229 ribosomal protein L31 ( rpmE ) 1.54 <0.001 BB0251 leucyl-tRNA synthetase ( leuS ) 3.41 <0.001 BB0514 phenylalanyl-tRNA synthetase, subunit ( pheT ) 1.63 0.009 BB0615 ribosomal protein S4 (...”
• Stage-specific global alterations in the transcriptomes of Lyme disease spirochetes during tick feeding and following mammalian host adaptation
  Iyer, Molecular microbiology 2015
  • “...Na+/H+ antiporter, NhaC-2 63 130 1528 435 bb0699 ribosomal protein L19 64 50 71 63 bb0229 ribosomal protein L31 65 36 60 90 bb0698 tRNA (guanine-N1)-methyltransferase 66 84 73 36 bb0749 hypothetical protein 67 190 519 281 bb0328 oligopeptide ABC transporter, periplasmic oligopeptide-binding protein, OppA1 68...”
• Proteome analysis of Borrelia burgdorferi response to environmental change
  Angel, PloS one 2010
  • “...ranging from 1.5 to 9 fold. Additionally, mediators of cell division FtsH (BB0789) and FtsZ (BB0229) were observed at reduced levels in the RpH culture. 10.1371/journal.pone.0013800.g005 Figure 5 Semi-quantitative analysis of protein abundance by spectral counting. A) Representative protein spectral count values show an increased abundance...”
• Combined effects of blood and temperature shift on Borrelia burgdorferi gene expression as determined by whole genome DNA array
  Tokarz, Infection and immunity 2004
  • “...BB0519 grpE protein (GrpE) BB103 hypothetical protein BB0229 ribosomal protein L31 (RpmE) BB0395 preprotein translocase subunit (SecE) BB102 conserved...”
• Profiling of temperature-induced changes in Borrelia burgdorferi gene expression by using whole genome arrays
  Ojaimi, Infection and immunity 2003
  • “...BBS37 BBQ42 BB0355 BBE10 BBA74 BBA28 BB0175 BB0631 BB0229 BB0562 BB0501 BB0703 BB0538 BB0803 BBB28 BB0541 BB0190 BBL35 BB0785 BBH29 BB0048 BBM38 BB0441 BB0423...”
  • “...BB0631 BB0044 BB0423 BB0562 BB0803 BB0541 BBF20 BB0061 BB0229 BB0441 BBE21 BBL35 BB0691 BB0501 BB0538 BB0190 BB0143 BBH29 BBM38 BBH16 BBI29 BBE10 BBB28 BB0338...”

PSPTO_4183 ribosomal protein L31 from Pseudomonas syringae pv. tomato str. DC3000
33% identity, 74% coverage

• Characterization of the Fur regulon in Pseudomonas syringae pv. tomato DC3000
  Butcher, Journal of bacteriology 2011
  • “...(csrA-3) PSPTO_4125-PSPTO_4124 and PSPTO_4126-PSPTO_4127 PSPTO_4183 PSPTO_4785-4786-4787 PSPTO_5311 PSPTO_5454 PSPTO_5484-PSPTO_5483 Overlaps MEME?d,e...”

KPNJ2_04207 type B 50S ribosomal protein L31 from Klebsiella pneumoniae 30684/NJST258_2
33% identity, 83% coverage

• Iron Acquisition and Siderophore Release by Carbapenem-Resistant Sequence Type 258 Klebsiella pneumoniae
  Holden, mSphere 2018
  • “...182.8 7.0 53.7 177.6 16.2 158.2 203.8 43.0 216.3 291.0 192.6 259.2 303.4 2.5 2.06E07 KPNJ2_04207 Ribosomal protein L31 116.7 57.1 34.4 28.7 17.3 29.3 97.7 28.8 48.8 220.6 22.7 35.5 240.5 26.1 41.6 2.0 1.51E06 KPNJ2_04728 Hypothetical protein 9.9 69.5 236.0 26.0 81.5 525.5 39.2...”

MSMEG_6070 ribosomal protein L31 from Mycobacterium smegmatis str. MC2 155
33% identity, 79% coverage

• Critical Role of Zur and SmtB in Zinc Homeostasis of Mycobacterium smegmatis
  Goethe, mSystems 2020
  • “...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 protein L31 MSMEG_6071 MAP0485c (66.9) <0.0001 5.2 Metallo-beta-lactamase superfamily protein MSMEG_6211 <0.0001 4.11 Hypothetical protein MSMEG_6237 <0.0001 7.4 Class I SAM-dependent methyl-transferase MSMEG_6610 <0.0001...”
  • “...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 MSMEG_0755....”
• Gene Expression, Bacteria Viability and Survivability Following Spray Drying of Mycobacterium smegmatis
  Lauten, Materials (Basel, Switzerland) 2010
  • “...L31 rpmE 0.8 13.8 0.005 37% MSMEG_5489 ribosomal protein L32 rpmF 1.1 11.1 0.010 22% MSMEG_6070 ribosomal protein L31 rpmE 0.0 10.1 0.704 0% MSMEG_6067 ribosomal protein 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...”

PFL_4896 ribosomal protein L31 from Pseudomonas fluorescens Pf-5
34% identity, 82% coverage

• Effect of tannic acid on the transcriptome of the soil bacterium Pseudomonas protegens Pf-5
  Lim, Applied and environmental microbiology 2013
  • “...S1 in the supplemental material). Among these is PFL_4896, which encodes the zincindependent form of ribosomal protein L31 (C form). In contrast, the transcript...”

B0JY33 Large ribosomal subunit protein bL31 from Microcystis aeruginosa (strain NIES-843 / IAM M-2473)
38% identity, 83% coverage

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

CTL0277 LSU ribosomal protein L31P from Chlamydia trachomatis 434/Bu
37% identity, 60% coverage

• Chlamydia trachomatis Alters Mitochondrial Protein Composition and Secretes Effector Proteins That Target Mitochondria
  Dimond, mSphere 2022
  • “...(%) MitoProt MTS prediction a CTL0259 (CT004) Aspartyl/glutamyl-tRNA amidotransferase subunit B, gatB 2 5 0.012 CTL0277 (CT022) Type B 50S ribosomal protein L31, rpmE2 2 24 0.047 CTL0283 (CT028) 50S ribosomal protein L19, rplS 3 26 0.146 CTL0301 (CT045) Leucyl aminopeptidase, pepA 4 8 0.015 CTL0321...”
• Genomewide Transcriptional Responses of Iron-Starved Chlamydia trachomatis Reveal Prioritization of Metabolic Precursor Synthesis over Protein Translation
  Brinkworth, mSystems 2018
  • “...A site, rescuing stalled ribosomes and tagging nascent peptides for degradation Unknown function rpmE Decrease CTL0277 L31 Ribosomal protein 23S rRNA Unknown rplQ Decrease CTL0768 L15 Ribosomal protein 23S rRNA Unknown rplY Decrease CTL0168 L25 Ribosomal protein 5S rRNA Binds to 5S in central protuberance a...”

ECA_RS05790 type B 50S ribosomal protein L31 from Pectobacterium atrosepticum SCRI1043
32% identity, 82% coverage

• Genome-Wide Analyses of the Temperature-Responsive Genetic Loci of the Pectinolytic Plant Pathogenic Pectobacterium atrosepticum
  Kaczynska, International journal of molecular sciences 2021
  • “...100; CAG74551.1; ECA_RS08155 ; MPU Hypothetical protein ECA1647 1.9 ENOG502FKDA WT 6 PbaTn5-A29 100; CAG74078.1; ECA_RS05790 ; PTU Putative 50S ribosomal protein L31 1.6 COG0254J WT 7 PbaTn5-B9 90; CAG73972.1; ECA_RS05265 ; PTU Putative integrase 2.1 COG4688S WT 8 PbaTn5-B16 100; CAG75691.1; ECA_RS13700 ; MTU Putative...”

AS87_RS03960, B739_1112 type B 50S ribosomal protein L31 from Riemerella anatipestifer Yb2
34% identity, 81% coverage

• Riemerella anatipestifer AS87_RS09170 gene is responsible for biotin synthesis, bacterial morphology and virulence
  Ren, Scientific reports 2018
  • “...haloacid dehalogenase 1.16 AS87_RS02380 ABC transporter ATP-binding protein 1.14 AS87_RS06190 ABC transporter ATP-binding protein 1.13 AS87_RS03960 type B 50S ribosomal protein L31 0.99 AS87_RS01395 transcription activator effector-binding protein 0.97 AS87_RS10270 hypothetical protein 0.96 AS87_RS02825 HIT family protein 0.96 AS87_RS07030 mannose-6-phosphate isomerase 0.95 AS87_RS10115 hypothetical protein 0.91...”
• Identifying the Genes Responsible for Iron-Limited Condition in Riemerella anatipestifer CH-1 through RNA-Seq-Based Analysis
  Liu, BioMed research international 2017
  • “...tRNA-Glu 13715606 B739_1068 3.8593 0 FecA 13715627 B739_1089 1.3526 1.76 E 65 Hypothetical protein 13715649 B739_1112 1.0673 5.05 E 41 50S ribosomal protein L31 13715783 B739_1246 1.0718 1.24 E 91 30S ribosomal protein S16 13715836 B739_1299 1.2361 5.75 E 09 Hypothetical protein 13715897 B739_1360 1.3576 0.0002407...”

RL31B_BACSU / O34967 Large ribosomal subunit protein bL31B; 50S ribosomal protein L31 type B from Bacillus subtilis (strain 168) (see paper)
NP_390948 ribosomal protein L31 from Bacillus subtilis subsp. subtilis str. 168
32% identity, 78% coverage

• function: While neither of the L31 paralogs is essential, this protein does not seem to function as the main L31 protein. Has a higher affinity for 70S ribosomes than the zinc-containing L31 paralog; is able to displace it to varying extents, even under zinc-replete conditions.
  subunit: Part of the 50S ribosomal subunit after the end of exponential growth.
• Contributions of Zur-controlled ribosomal proteins to growth under zinc starvation conditions.
  Gabriel, Journal of bacteriology 2009
  • GeneRIF: The results support a direct and physiologically relevant role for YtiA in mobilizing zinc from ribosomes.
• Proteomics analyses of Bacillus subtilis after treatment with plumbagin, a plant-derived naphthoquinone
  Reddy, Omics : a journal of integrative biology 2015
  • “...ribosomal protein L3 OS P19947 50S ribosomal protein L30 OS O34967 50S ribosomal protein L31 type B OS P55874 50S ribosomal protein L35 OS a Gene name Q-TOF...”

MAB_0336 50S ribosomal protein L31 type B from Mycobacterium abscessus ATCC 19977
32% identity, 81% coverage

• 2-Aminoimidazoles Inhibit Mycobacterium abscessus Biofilms in a Zinc-Dependent Manner
  Belardinelli, International journal of molecular sciences 2022
  • “...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 MAB_1680 to...”
  • “...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 MAB_0575c Putative ABC-transporter transmembrane protein ZnuABC transporter (Zn import) 2.91 2.39 MAB_0576c Putative ABC-transporter ATP-binding protein 4.05 2.89 MAB_0577c...”

PA14_17700 putative ribosomal protein, L31P family from Pseudomonas aeruginosa UCBPP-PA14
PA3601 hypothetical protein from Pseudomonas aeruginosa PAO1
IS492_27315 type B 50S ribosomal protein L31 from Pseudomonas aeruginosa
38% identity, 84% coverage

• Activity of N-Acetylcysteine Alone and in Combination with Colistin against Pseudomonas aeruginosa Biofilms and Transcriptomic Response to N-Acetylcysteine Exposure
  Valzano, Microbiology spectrum 2022
  • “...PA14_17710 rpmJ2 Zinc-independent paralog type B 50S ribosomal protein L36 + 2.0E16 1.3 IS492_27315 PA3601 PA14_17700 rpmE2 Zinc-independent paralog type B 50S ribosomal protein L31 + 1.2E04 0.7 IS492_29825 PA4063 PA14_11320 Zinc SBP (zinc uptake) + 7.0E41 2.0 IS492_29830 PA4064 PA14_11310 Zinc ABC transporter, ATP-binding protein...”
• Elucidating Essential Genes in Plant-Associated Pseudomonas protegens Pf-5 Using Transposon Insertion Sequencing
  Fabian, Journal of bacteriology 2021 (secret)
• Loss of the Two-Component System TctD-TctE in Pseudomonas aeruginosa Affects Biofilm Formation and Aminoglycoside Susceptibility in Response to Citric Acid
  Taylor, mSphere 2019
  • “...PA14_61600 2.68 PA14_61610 2.60 PA14_44480 2.57 PA14_02520 2.54 PA14_45620 cheY Two-component response regulator CheY 2.48 PA14_17700 2.48 PA14_10730 2.44 PA14_24770 2.38 PA14_68260 2.36 PA14_45610 cheZ Chemotaxis protein CheZ 2.29 PA14_16260 2.29 PA14_15030 leuA 2-Isopropylmalate synthase 2.28 PA14_61840 2.28 PA14_60520 2.26 PA14_16680 2.19 PA14_30830 2.17 PA14_44860 2.15...”
• Contribution of Veillonella parvula to Pseudomonas aeruginosa-mediated pathogenicity in a murine tumor model system
  Pustelny, Infection and immunity 2015
  • “...PA14_39650 PA14_17710 PA14_15070 PA14_73020 PA14_10200 PA14_17700 PA14_58030 PA14_66510 PA14_09260 PA14_01720 PA14_15120 PA14_53290 PA14_72970 PA14_27520...”
• Activity of N-Acetylcysteine Alone and in Combination with Colistin against Pseudomonas aeruginosa Biofilms and Transcriptomic Response to N-Acetylcysteine Exposure
  Valzano, Microbiology spectrum 2022
  • “...PA3600 PA14_17710 rpmJ2 Zinc-independent paralog type B 50S ribosomal protein L36 + 2.0E16 1.3 IS492_27315 PA3601 PA14_17700 rpmE2 Zinc-independent paralog type B 50S ribosomal protein L31 + 1.2E04 0.7 IS492_29825 PA4063 PA14_11320 Zinc SBP (zinc uptake) + 7.0E41 2.0 IS492_29830 PA4064 PA14_11310 Zinc ABC transporter, ATP-binding...”
• Global Analysis of the Zinc Homeostasis Network in Pseudomonas aeruginosa and Its Gene Expression Dynamics
  Ducret, Frontiers in microbiology 2021
  • “...paralogs dksA PA4723 Supressor protein dksA2 PA5536 Supressor protein rpmE PA5049 Ribosomal protein L31 rpmE2 PA3601 Ribosomal protein L31 rpmJ PA4242 Ribosomal protein L36 rpmJ2 PA3600 Ribosomal protein L36 Others PA2807 PA2807 Copper binding protein oprD PA0958 Outer membrane porin Zn Export Systems Dynamics of CadA...”
• Strategies for Zinc Uptake in Pseudomonas aeruginosa at the Host-Pathogen Interface
  Wang, Frontiers in microbiology 2021
  • “...in P. aeruginosa under zinc-restricted culture also showed that the expression of rpmE2 (PA3600), rpmJ2 (PA3601), and dksA2 (PA5536) was significantly upregulated ( Pederick et al., 2015 ; Gonzalez et al., 2018 ). RpmE2 and RpmJ2 are homologous proteins of the 50S ribosomal proteins RpmE (PA5049)...”
• Determination of the two-component systems regulatory network reveals core and accessory regulations across Pseudomonas aeruginosa lineages
  Trouillon, Nucleic acids research 2021
  • “...binding to one promoter. Among the most targeted genes are uncharacterized genes ( PA0123 and PA3601 ) but mostly well-characterized genes involved in bacterial survival and virulence (i.e. flp , encoding the type IVb pilin, the nuoA-N operon involved in the electron transport chain, zipA ,...”
• Calprotectin-Mediated Zinc Chelation Inhibits Pseudomonas aeruginosa Protease Activity in Cystic Fibrosis Sputum
  Vermilyea, Journal of bacteriology 2021 (secret)
• ZnuA and zinc homeostasis in Pseudomonas aeruginosa
  Pederick, Scientific reports 2015
  • “...2+ -binding resides (either His or Cys). The C isoforms L36 and L31 (PA3600 and PA3601, respectively) are predicted to be co-transcribed under the control of an adjacent putative Zur site ( P =0.0013), and lack almost all of the Zn 2+ -binding residues. Consistent with...”
  • “...hypothetical 4.1 PA3283 hypothetical 5.0 PA3284 hypothetical 5.0 PA3600 50S ribosomal protein L36 89.2 0.0013 PA3601 50S ribosomal protein L31 109.0 PA4063 Zn 2+ periplasmic binding protein 45.1 0.0011 PA4064 ABC transporter nucleotide binding protein 17.2 PA4065 lipoprotein release ABC transporter permease 22.1 PA4066 lipoprotein 10.6...”
• A novel siderophore system is essential for the growth of Pseudomonas aeruginosa in airway mucus
  Gi, Scientific reports 2015
  • “...PA3600 49.03 conserved hypothetical protein/Translation, post-translational modification PA0284 36.28 hypothetical protein PA4063 35.15 hypothetical protein PA3601 24.27 conserved hypothetical protein/Translation, post-translational modification PA2359 21.93 probable transcriptional regulator PA3450 21.63 probable antioxidant protein/adaptation, protection PA4570 19.36 hypothetical protein PA4471 18.45 hypothetical protein PA2161 16.99 hypothetical protein PA0802...”
• Inhibition of Pseudomonas aeruginosa swarming motility by 1-naphthol and other bicyclic compounds bearing hydroxyl groups
  Oura, Applied and environmental microbiology 2015
  • “...PA1679 PA1874 PA1914 PA3369 PA3370 PA3371 PA3488 PA3520 PA3601 PA3919 PA3923 PA3969 PA4063 PA4115 PA4155 PA4220 PA4648 PA4773 PA4774 PA4916 PA5460 PA5481 a Fold...”
• More
• Activity of N-Acetylcysteine Alone and in Combination with Colistin against Pseudomonas aeruginosa Biofilms and Transcriptomic Response to N-Acetylcysteine Exposure
  Valzano, Microbiology spectrum 2022
  • “...IS492_27310 PA3600 PA14_17710 rpmJ2 Zinc-independent paralog type B 50S ribosomal protein L36 + 2.0E16 1.3 IS492_27315 PA3601 PA14_17700 rpmE2 Zinc-independent paralog type B 50S ribosomal protein L31 + 1.2E04 0.7 IS492_29825 PA4063 PA14_11320 Zinc SBP (zinc uptake) + 7.0E41 2.0 IS492_29830 PA4064 PA14_11310 Zinc ABC transporter,...”

SMDB11_RS01845 type B 50S ribosomal protein L31 from Serratia marcescens subsp. marcescens Db11
31% identity, 85% coverage

• RNA‑seq analyses of antibiotic resistance mechanisms in Serratia marcescens
  Li, Molecular medicine reports 2019
  • “...0.028114887 SMDB11_RS09335 13 SMDB11_RS23570 1013.2664 SMDB11_RS23335 0.028103517 SMDB11_RS00625 13 SMDB11_RS21855 1010 SMDB11_RS14910 0.028103517 SMDB11_RS02545 13 SMDB11_RS01845 915.4805 SMDB11_RS02550 0.028097836 SMDB11_RS14100 13 SMDB11_RS05590 890.28687 SMDB11_RS00615 0.028080808 SMDB11_RS14095 12 SMDB11_RS03340 874.0195 SMDB11_RS00620 0.028075136 SMDB11_RS22005 10 SMDB11_RS14915 855.25476 SMDB11_RS00600 0.028075136 SMDB11_RS22020 10 SMDB11_RS02545 767.4091 SMDB11_RS02555 0.028075136 SMDB11_RS14105 10 SMDB11_RS00590...”

YPK_3210 ribosomal protein L31 from Yersinia pseudotuberculosis YPIII
YPO3134 putative ribosomal protein from Yersinia pestis CO92
y1048 50S ribosomal protein L31 type B from Yersinia pestis KIM
31% identity, 78% coverage

• Functional versatility of Zur in metal homeostasis, motility, biofilm formation, and stress resistance in Yersinia pseudotuberculosis
  Gu, Microbiology spectrum 2024
  • “...on these molecular metabolic pathways. Moreover, Zur negatively regulated the large subunit ribosomal protein bL31-B (YPK_3210) and bL36-B (YPK_3211), which are implicated in both ribosome assembly during translation and zinc homeostasis ( 42 , 43 ). The fact that Zur affects numerous metabolic pathways emphasizes its...”
  • “...in Y. pseudotuberculosis . ( A ) qRT-PCR analysis of mRNA levels of bL31-B ( ypk_3210 ), ddl ( ypk_3616 ), deoD ( ypk_3524 ), and deoC ( ypk_3627 ). ( B ) EMSA was performed to analyze the interactions between His6-Zur and various promoters (...”
• Characterization of Zur-dependent genes and direct Zur targets in Yersinia pestis
  Li, BMC microbiology 2009
  • “...marching of the Zur consensus Position of DNA fragment used Position Sequence Score EMSA Footprinting YPO3134 ykgM -34 to -16 GATGTTACATTATAACATA 15.6 -134 to +102 -134 to +102 YPO2060 znuC -45 to -27 AGCGTAATATTATAACATT 12.5 -185 to +52 -142 to +52 YPO2061 znuA -49 to -31...”
  • “...conditions [ 35 ]. The paralogous pairs of L31 protein are RpmE (YPO0111) and YkgM (YPO3134) in Y. pestis , while those of L36 protein are RpmJ (YPO0230) and RpmJ2 (YPO3135) [ 17 ]. YkgM and RpmJ2 are the C- forms of corresponding ribosomal proteins. ykgM...”
• Global gene expression profiling of Yersinia pestis replicating inside macrophages reveals the roles of a putative stress-induced operon in regulating type III secretion and intracellular cell division
  Fukuto, Infection and immunity 2010
  • “...in expression level Survival of deletion mutant in BMMsc y1048 y0464 y2316 y2662 y2127 y2315 y2126 YPO1507 y1430 y0510 y2313 y2880 YPO3135 y0740 y2127 y1048...”

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How It Works

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

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

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

PaperBLAST also incorporates manually-curated protein functions:

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

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

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

Changes to PaperBLAST since the paper was written:

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

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

Secrets

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

Omissions from the PaperBLAST Database

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

References

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

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

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

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

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

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

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

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

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

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

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

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