PaperBLAST
PaperBLAST Hits for EX31_RS22465 (84 a.a., MKPTIHPAYR...)
Show query sequence
>EX31_RS22465
MKPTIHPAYRTVVFHDTSADEYFKVGSTISTDRTIELEGATYPYISIEVSSASHPYYTGK
QKEYSKEGSTARFNQRFGSFLGKK
Running BLASTp...
Found 98 similar proteins in the literature:
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
79% identity, 98% 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...”
SMDB11_RS01845 type B 50S ribosomal protein L31 from Serratia marcescens subsp. marcescens Db11
77% identity, 100% 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...”
ECA_RS05790 type B 50S ribosomal protein L31 from Pectobacterium atrosepticum SCRI1043
81% identity, 96% coverage
KPNJ2_04207 type B 50S ribosomal protein L31 from Klebsiella pneumoniae 30684/NJST258_2
73% identity, 97% coverage
ESA_RS12970 type B 50S ribosomal protein L31 from Cronobacter sakazakii ATCC BAA-894
73% identity, 98% 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...”
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
69% identity, 97% 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...”
B7L427 Large ribosomal subunit protein bL31B from Escherichia coli (strain 55989 / EAEC)
69% identity, 97% coverage
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
69% identity, 98% coverage
VC0878 ribosomal protein, L31P family from Vibrio cholerae O1 biovar eltor str. N16961
69% identity, 94% coverage
VP_RS11315 type B 50S ribosomal protein L31 from Vibrio parahaemolyticus RIMD 2210633
VP2331 ribosomal protein, L31P family from Vibrio parahaemolyticus RIMD 2210633
65% identity, 98% coverage
U876_13185 type B 50S ribosomal protein L31 from Aeromonas hydrophila NJ-35
63% identity, 93% coverage
PSPTO_4183 ribosomal protein L31 from Pseudomonas syringae pv. tomato str. DC3000
63% identity, 86% coverage
B7C60_RS12925 type B 50S ribosomal protein L31 from Vibrio fujianensis
65% identity, 95% coverage
Psyr_3920 Ribosomal protein L31 from Pseudomonas syringae pv. syringae B728a
60% identity, 90% coverage
6i7vD7 / P0A7N1 6i7vD7 (see paper)
72% identity, 81% coverage
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
59% identity, 97% 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,...”
PFL_4896 ribosomal protein L31 from Pseudomonas fluorescens Pf-5
60% identity, 90% coverage
HMPREF0010_01851 type B 50S ribosomal protein L31 from Acinetobacter baumannii ATCC 19606 = CIP 70.34 = JCM 6841
A1S_0391 50S ribosomal protein L31 type B from Acinetobacter baumannii ATCC 17978
ABBFA_003147 ribosomal protein L31 from Acinetobacter baumannii AB307-0294
55% identity, 95% coverage
- Delineating the Plausible Molecular Vaccine Candidates and Drug Targets of Multidrug-Resistant Acinetobacter baumannii
Mujawar, Frontiers in cellular and infection microbiology 2019 - “...A1S_0063 HMPREF0010_03221 A1S_0114 HMPREF0010_03191 A1S_0147 HMPREF0010_02008 A1S_0217 HMPREF0010_01991 A1S_0236 HMPREF0010_01903 A1S_0334 HMPREF0010_01875 A1S_0364 HMPREF0010_01854 A1S_0388 HMPREF0010_01851 A1S_0391 HMPREF0010_01810 A1S_0428 HMPREF0010_01791 A1S_0447 HMPREF0010_01758 A1S_0469 HMPREF0010_01757 A1S_0470 HMPREF0010_01723 A1S_0506 HMPREF0010_01691 A1S_0561 HMPREF0010_01682 A1S_0571 KFC HMPREF0010_02522 HMPREF0010_02769 HMPREF0010_03233 HMPREF0010_00091 A1S_2232 HMPREF0010_03207 HMPREF0010_01641 HMPREF0010_03022 HMPREF0010_02437 A1S_3280 HMPREF0010_01350 HMPREF0010_01047 Table 6...”
- Colistin-resistant, lipopolysaccharide-deficient Acinetobacter baumannii responds to lipopolysaccharide loss through increased expression of genes involved in the synthesis and transport of lipoproteins, phospholipids, and poly-β-1,6-N-acetylglucosamine
Henry, Antimicrobial agents and chemotherapy 2012 - “...HMPREF0010_02568 HMPREF0010_03355 HMPREF0010_02269 HMPREF0010_01851 HMPREF0010_03241 HMPREF0010_02727 HMPREF0010_03242 HMPREF0010_03516 HMPREF0010_02675...”
- A corepressor participates in LexA-independent regulation of error-prone polymerases in Acinetobacter
Peterson, Microbiology (Reading, England) 2020 - “...in ddrR mutant Repressed in wild type*? A1S_0292 put. outer membrane protein W 1.69 yes A1S_0391 50S ribosomal protein L31 type B 2.70 A1S_0548 put. transcriptional regulator (TetR family) 1.50 yes A1S_0549 hypothetical 1.42 yes A1S_0891 hemerythrin-like metal-binding protein 1.71 yes A1S_1216 A1S_1217 A1S_1218 LysR regulator...”
- Delineating the Plausible Molecular Vaccine Candidates and Drug Targets of Multidrug-Resistant Acinetobacter baumannii
Mujawar, Frontiers in cellular and infection microbiology 2019 - “...HMPREF0010_03221 A1S_0114 HMPREF0010_03191 A1S_0147 HMPREF0010_02008 A1S_0217 HMPREF0010_01991 A1S_0236 HMPREF0010_01903 A1S_0334 HMPREF0010_01875 A1S_0364 HMPREF0010_01854 A1S_0388 HMPREF0010_01851 A1S_0391 HMPREF0010_01810 A1S_0428 HMPREF0010_01791 A1S_0447 HMPREF0010_01758 A1S_0469 HMPREF0010_01757 A1S_0470 HMPREF0010_01723 A1S_0506 HMPREF0010_01691 A1S_0561 HMPREF0010_01682 A1S_0571 KFC HMPREF0010_02522 HMPREF0010_02769 HMPREF0010_03233 HMPREF0010_00091 A1S_2232 HMPREF0010_03207 HMPREF0010_01641 HMPREF0010_03022 HMPREF0010_02437 A1S_3280 HMPREF0010_01350 HMPREF0010_01047 Table 6 The...”
- Identification of an Acinetobacter baumannii zinc acquisition system that facilitates resistance to calprotectin-mediated zinc sequestration
Hood, PLoS pathogens 2012 - “...Locus tag Description 1 E value 2 A1S_0145 Zur (ZnuB, ZnuC) 6.19e-08 A1S_0146 ZnuA 9.90e-08 A1S_0391 LSU ribosomal protein L31p 5.74e-07 A1S_0410 LysR family transcriptional regulator 3.12e-06 A1S_0452 TonB (ExbB, ExbD) 1.17e-07 A1S_1679 Hypothetical protein 1.42e-05 A1S_2829 Putative TonB-dependent receptor 1.84e-05 A1S_2892 Putative TonB-dependent receptor, ZnuD1...”
- Polymyxin Resistance in Acinetobacter baumannii: Genetic Mutations and Transcriptomic Changes in Response to Clinically Relevant Dosage Regimens
Cheah, Scientific reports 2016 - “...oprM precursor 2.51 1.46 1.11 1.78 0.036 ABBFA_003050 phosphogluconate dehydratase 1.45 0.88 0.61 1.29 0.050 ABBFA_003147 50S ribosomal protein L31 type B 2.07 1.71 1.20 1.39 0.037 ABBFA_003406 AMP-binding enzyme family protein 1.59 0.89 0.87 1.88 0.050 ABBFA_003500 Hypothetical protein Lipoprotein 3.28 0.64 2.07 2.69 0.050...”
Rmet_2137 type B 50S ribosomal protein L31 from Cupriavidus metallidurans CH34
57% identity, 95% coverage
gbs0581 50S ribosomal protein L31 from Streptococcus agalactiae NEM316
54% identity, 91% coverage
SMU_1298 type B 50S ribosomal protein L31 from Streptococcus mutans UA159
53% identity, 93% coverage
SSA_1272 50S ribosomal protein L31 type B, putative from Streptococcus sanguinis SK36
51% identity, 93% coverage
SPD_1154 ribosomal protein L31 from Streptococcus pneumoniae D39
SP_1299 50S ribosomal protein L31 type B from Streptococcus pneumoniae TIGR4
51% identity, 93% 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...”
STER_0787, STER_RS03860 type B 50S ribosomal protein L31 from Streptococcus thermophilus
51% identity, 93% 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...”
bglu_1g14290 Ribosomal protein L31 from Burkholderia glumae BGR1
53% identity, 92% coverage
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
53% identity, 93% 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)
53% identity, 93% coverage
BTH_I2213 50S ribosomal protein L31 type B from Burkholderia thailandensis E264
52% identity, 91% coverage
NMB0942 50S ribosomal protein L31 from Neisseria meningitidis MC58
48% identity, 89% coverage
BAS5180 ribosomal protein L31 from Bacillus anthracis str. Sterne
BA5574 ribosomal protein L31 from Bacillus anthracis str. Ames
48% identity, 93% coverage
NMA1138 putative additional 50S ribosomal protein L31 from Neisseria meningitidis Z2491
48% identity, 89% coverage
BPSL1491 50S ribosomal protein L31 from Burkholderia pseudomallei K96243
52% identity, 91% 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...”
LLNZ_04655 type B 50S ribosomal protein L31 from Lactococcus cremoris subsp. cremoris NZ9000
49% identity, 93% coverage
5myjB3 / A2RJP7 of 70S ribosome from Lactococcus lactis (see paper)
49% identity, 93% coverage
B4RL59 Large ribosomal subunit protein bL31B from Neisseria gonorrhoeae (strain NCCP11945)
46% identity, 89% coverage
SCO3427 50S ribosomal protein L31 from Streptomyces coelicolor A3(2)
47% identity, 93% coverage
SERP1727 ribosomal protein L31 from Staphylococcus epidermidis RP62A
48% identity, 92% coverage
AS87_RS03960, B739_1112 type B 50S ribosomal protein L31 from Riemerella anatipestifer Yb2
49% identity, 95% coverage
PD0749 50S ribosomal protein L31 from Xylella fastidiosa Temecula1
47% identity, 93% coverage
RL31B_LACPL / Q88Z52 Large ribosomal subunit protein bL31B; 50S ribosomal protein L31 type B from Lactiplantibacillus plantarum (strain ATCC BAA-793 / NCIMB 8826 / WCFS1) (Lactobacillus plantarum) (see paper)
lp_0512 type B 50S ribosomal protein L31 from Lactiplantibacillus plantarum WCFS1
lp_0512 ribosomal protein L31 from Lactobacillus plantarum WCFS1
47% identity, 93% coverage
- subunit: Part of the 50S ribosomal subunit.
- Transcriptional analysis of the molecular mechanism underlying the response of Lactiplantibacillus plantarum to lactic acid stress conditions
Jang, Heliyon 2023 - “...transcriptional regulator lp_1153 COG1309 rpmE2 2.29 2.62E-16 1.37E-14 1.47 6.65E-08 1.15E-06 50S ribosomal protein L31 lp_0512 COG0254 lp_2526 2.16 1.16E-26 9.93E-25 1.49 4.32E-14 1.61E-12 GNAT family acetyltransferase lp_2526 COG0454 lp_1900 2.64 1.35E-21 9.35E-20 1.50 1.59E-08 3.07E-07 membrane protein lp_1900 ENOG502DGWH cspC 2.26 6.84E-13 2.79E-11 1.66 7.39E-08...”
- Inorganic phosphate modifies stationary phase fitness and metabolic pathways in Lactiplantibacillus paraplantarum CRL 1905
Araoz, Frontiers in microbiology 2024 - “...and biogenesis frr Q88VJ7 Ribosome-recycling factor * rplW Q88XY4 50S ribosomal protein L23 * rpmE2 Q88Z52 50S ribosomal protein L31 5.7 Function unknown lp_2350 F9UQQ2 Lipoprotein * lp_2229 F9UQF3 Metal-dependent hydrolase, beta-lactamase superfamily II * lp_2260 F9UQH9 Extracellular protein, DUF336 * lp_0221 F9UT26 Family 2,5 diketo-D-gluconic...”
- The regulation of simulated artificial oro-gastrointestinal transit stress on the adhesion of Lactobacillus plantarum S7.
Chen, Microbial cell factories 2023 - “...protein L14 rplN 2.51 2.76 A0A660DXH6 50S ribosomal protein L10 [Lactobacillus sp.] MUDAN_MDHGFNIF_00600 4.99 5.24 Q88Z52 50S ribosomal protein L31 type B rpmE2 1.32 1.31 A0A0R2DQ84 50S ribosomal protein L7/L12 rpmF 0.71 0.74 A0A6N9I1Z5 50S ribosomal protein L32 rpsL 0.52 0.50 Q88WS9 50S ribosomal protein L32...”
- Heat shock response in Lactobacillus plantarum.
De, Applied and environmental microbiology 2004 (no snippet) - Transcriptional Reprogramming at Genome-Scale of Lactobacillus plantarum WCFS1 in Response to Olive Oil Challenge
Esteban-Torres, Frontiers in microbiology 2017 - “...oxidative stress included upregulation of the gene coding for the ribosomal protein 50S L31 ( lp_0512 ) which has been previously reported to respond to thiol stress ( Paget et al., 2001 ). Elements Typically Involved in the Stringent Response are Responsive to EVOO Genes related...”
- “...[RPL5], lp_1048 [RPS14], lp_1052 [RPL18], lp_1053 [RPS5], lp_1061 [RPS11]) and six upregulated ( lp_0009 [RPS6], lp_0512 [RPL31], lp_0737 [RPS30A], lp_1636 [RPS16], lp_1973 [RPS21], lp_2126 [RPS20]). In addition, genes coding for cell division proteins [ lp_0542 ( divIC , septum formation initiator) and lp_2272 ( zapA ,...”
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
45% identity, 99% coverage
SCO1150 50S ribosomal protein L31 from Streptomyces coelicolor A3(2)
45% identity, 92% 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...”
EF1171 ribosomal protein L31 from Enterococcus faecalis V583
IUJ47_RS08865 type B 50S ribosomal protein L31 from Enterococcus faecalis
47% identity, 88% 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)
47% identity, 93% coverage
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)
46% identity, 93% coverage
5li03 / Q2FWD8 5li03 (see paper)
46% identity, 93% coverage
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)
42% identity, 95% coverage
C9Z0W5 Large ribosomal subunit protein bL31B from Streptomyces scabiei (strain 87.22)
SCAB_39991 putative 50S ribosomal protein L31 from Streptomyces scabiei 87.22
44% identity, 99% coverage
LSEI_2569 Ribosomal protein L31 from Lactobacillus casei ATCC 334
46% identity, 93% coverage
E2P69_RS10215, XAC29_17265 type B 50S ribosomal protein L31 from Xanthomonas axonopodis Xac29-1
42% identity, 93% coverage
PMCN03_1019 type B 50S ribosomal protein L31 from Pasteurella multocida subsp. multocida str. HB03
45% identity, 91% coverage
APL_1821 50S ribosomal protein L31 from Actinobacillus pleuropneumoniae L20
43% identity, 92% coverage
- Biofilm formation by virulent and non-virulent strains of Haemophilus parasuis
Bello-Ortí, Veterinary research 2014 - “...Product HS372_02083 APL_1425 Cytochrome c-type protein NapC HS372_02085 APL_1427 Putative electron transport protein yccM HS372_02091 APL_1821 50S ribosomal protein L31 type B HS372_00945 APL_1440 High-affinity zinc uptake system protein znuA precursor HS372_00147 APL_1894 hypothetical protein HS372_02009 APL_1423 Putative esterase HS372_02012 APL_0433 Peptide methionine sulfoxide reductase MsrB...”
- Effects of growth conditions on biofilm formation by Actinobacillus pleuropneumoniae
Labrie, Veterinary research 2010 - “...Disulfide bond formation protein B 1.557 APL_1035 pflA Pyruvate formate-lyase 1-activating enzyme 1.774 Protein synthesis APL_1821 rpmE 50S ribosomal protein L31 2.211 APL_0484 rimK Ribosomal protein S6 modification protein 1.533 APL_1781 rpsM 30S ribosomal protein S13 1.401 APL_0205 APL_0205 Predicted rRNA methyltransferase 1.538 APL_0399 ksgA Dimethyladenosine...”
CTL0277 LSU ribosomal protein L31P from Chlamydia trachomatis 434/Bu
43% identity, 71% coverage
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
41% identity, 81% 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...”
MAB_0336 50S ribosomal protein L31 type B from Mycobacterium abscessus ATCC 19977
43% identity, 94% 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...”
BB0229 ribosomal protein L31 (rpmE) from Borrelia burgdorferi B31
40% identity, 92% 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...”
8uu93 / A0A0U4MT39 8uu93 (see paper)
49% identity, 92% coverage
FN0482 LSU ribosomal protein L31P from Fusobacterium nucleatum subsp. nucleatum ATCC 25586
40% identity, 100% 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,...”
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
43% identity, 99% coverage
8rd8fJ / A0A0M4SX87 8rd8fJ (see paper)
53% identity, 65% coverage
FP1135 50S ribosomal protein L31 type B from Flavobacterium psychrophilum JIP02/86
IA01_05395 type B 50S ribosomal protein L31 from Flavobacterium psychrophilum
41% identity, 93% coverage
- Stress Tolerance-Related Genetic Traits of Fish Pathogen Flavobacterium psychrophilum in a Mature Biofilm
Levipan, Frontiers in microbiology 2018 - “...GO:0006355 4.06 FP0994 Probable transcriptional regulator, AraC family FPSM_01394, FP0994 GO:0003700, GO:0043565, GO:0006351, GO:0006355 3.38 FP1135 50S ribosomal protein L31 IA01_05395, rpmE GO:0005840, GO:0003735, GO:0006412 3.69 FP1175 DNA-directed RNA polymerase beta' subunit RpoC rpoC GO:0003677, GO:0003899, GO:0006351 2.65 FP1176 DNA-directed RNA polymerase beta subunit RpoB rpoB...”
- Stress Tolerance-Related Genetic Traits of Fish Pathogen Flavobacterium psychrophilum in a Mature Biofilm
Levipan, Frontiers in microbiology 2018 - “...regulator, AraC family FPSM_01394, FP0994 GO:0003700, GO:0043565, GO:0006351, GO:0006355 3.38 FP1135 50S ribosomal protein L31 IA01_05395, rpmE GO:0005840, GO:0003735, GO:0006412 3.69 FP1175 DNA-directed RNA polymerase beta' subunit RpoC rpoC GO:0003677, GO:0003899, GO:0006351 2.65 FP1176 DNA-directed RNA polymerase beta subunit RpoB rpoB GO:0003677, GO:0003899, GO:0032549, GO:0006351 2.65...”
FE46_RS09965 type B 50S ribosomal protein L31 from Flavobacterium psychrophilum
41% identity, 93% coverage
AMUC_RS07650 type B 50S ribosomal protein L31 from Akkermansia muciniphila ATCC BAA-835
37% identity, 87% 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...”
CT022 L31 Ribosomal Protein from Chlamydia trachomatis D/UW-3/CX
44% identity, 71% 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 (CT065)...”
- Antibodies to Variable Domain 4 Linear Epitopes of the Chlamydia trachomatis Major Outer Membrane Protein Are Not Associated with Chlamydia Resolution or Reinfection in Women
Collar, mSphere 2020 - “...2 4 Hypothetical protein CT143 QAYNCATHRNG 123133 13 9/30 3 4 2 L31 ribosomal protein CT022 CGSTYQTDKT 2534 12 11/30 5 3 3 CHLPN 76-kDa homolog CT622 LKQEHTGLTD 283292 12 9/30 5 2 2 Hypothetical protein CT695 RTTSSSGVSED 5767 11 9/30 3 3 3 Aspartyl tRNA...”
- Identification of Chlamydia trachomatis Antigens Recognized by T Cells From Highly Exposed Women Who Limit or Resist Genital Tract Infection
Russell, The Journal of infectious diseases 2016 - “...3.30 .060 CT351 . . . Hypothetical protein 0.273 3.32 .061 CT022 rI31 50S ribosomal protein L31 0.291 2.68 .065 CT133 . . . rRNA methylase 0.345 2.44 .068 CT687...”
- Chlamydia trachomatis antigens recognized in women with tubal factor infertility, normal fertility, and acute infection
Budrys, Obstetrics and gynecology 2012 - “...23), CT694 (a putative effector of the type III secretion pathway; ref: ( 24 ), CT022 (50S ribosomal protein L31 type B), and CT806 (insulinase family/protease III, Ptr). These proteins were designated as immunodominant antigens in these women. The reactivity of each of the 908 C....”
- BLAST screening of chlamydial genomes to identify signature proteins that are unique for the Chlamydiales, Chlamydiaceae, Chlamydophila and Chlamydia groups of species
Griffiths, BMC genomics 2006 - “...(49%) CT019 IleRS 1036/1036 (100%) 923/1036 (89%) 715/1043 (68%) 729/1043 (69%) 729/1043 (69%) 575/1038 (55%) CT022 Ribo. L31 108/108 (100%) 103/108 (95%) 90/109 (81%) 87/208 (80%) 86/108 (79%) 67/117 (57%) CT034 YtfF 341/341 (100%) 279/341 (81%) 183/338 (53%) 203/338 (59%) 203/339 (59%) 94/281 (27%) Average 100%...”
7p48Y / A0A380EL30 7p48Y (see paper)
41% identity, 93% coverage
MSMEG_6070 ribosomal protein L31 from Mycobacterium smegmatis str. MC2 155
40% identity, 93% 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...”
SO4120, SO_4120 ribosomal protein L31 from Shewanella oneidensis MR-1
38% identity, 100% coverage
A0J47_RS02550, VDA_003390 50S ribosomal protein L31 from Photobacterium damselae subsp. damselae
36% identity, 99% coverage
7nhl4 / Q2FWD8 7nhl4 (see paper)
39% identity, 90% coverage
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
34% identity, 92% coverage
8cd1Le / Q9HUD0 8cd1Le (see paper)
35% identity, 95% coverage
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
35% identity, 95% 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 [...”
PFL_0441 ribosomal protein L31 from Pseudomonas fluorescens Pf-5
32% identity, 95% coverage
PP_5087 ribosomal protein L31 from Pseudomonas putida KT2440
36% identity, 100% coverage
- H-NS Family Proteins Drastically Change Their Targets in Response to the Horizontal Transfer of the Catabolic Plasmid pCAR1
Nakamura, Frontiers in microbiology 2020 - “...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...”
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
32% identity, 92% 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
32% identity, 92% coverage
VC2679 ribosomal protein L31 from Vibrio cholerae O1 biovar eltor str. N16961
33% identity, 100% coverage
ACIAD2210 50S ribosomal protein L31 from Acinetobacter sp. ADP1
36% identity, 92% coverage
KF946_12560 50S ribosomal protein L31 from Idiomarina loihiensis
37% identity, 100% coverage
VP0255 ribosomal protein L31 from Vibrio parahaemolyticus RIMD 2210633
34% identity, 95% coverage
EAMY_0136 50S ribosomal protein L31 from Erwinia amylovora CFBP1430
32% identity, 92% coverage
HSM_0533 50S ribosomal protein L31 from Histophilus somni 2336
HSM_0533 ribosomal protein L31 from Haemophilus somnus 2336
32% identity, 92% coverage
Asuc_0525 ribosomal protein L31 from Actinobacillus succinogenes 130Z
34% identity, 92% 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...”
MT1337 50S ribosomal protein L31 from Mycobacterium tuberculosis CDC1551
Rv1298 50S ribosomal protein L31 from Mycobacterium tuberculosis H37Rv
40% identity, 93% 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 -...”
B7C60_RS02450 50S ribosomal protein L31 from Vibrio fujianensis
35% identity, 100% coverage
MAB_1441 50S ribosomal protein L31 from Mycobacterium abscessus ATCC 19977
37% identity, 93% coverage
7jila / A0A1M5KIG2 7jila (see paper)
43% identity, 68% coverage
HI0758 ribosomal protein L31 (rpL31) from Haemophilus influenzae Rd KW20
34% identity, 92% coverage
APL_0982 50S ribosomal protein L31 from Actinobacillus pleuropneumoniae L20
31% identity, 92% coverage
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)
40% identity, 93% 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)...”
SYNW2095 50S ribosomal protein L31 from Synechococcus sp. WH 8102
30% identity, 97% coverage
9c4g4 / A0A2B7JUW7 Cutibacterium acnes 50s ribosomal subunit with clindamycin bound (see paper)
35% identity, 93% coverage
5zeb2 / A0R215 5zeb2 (see paper)
38% identity, 93% coverage
MSMEG_4951 50S ribosomal protein L31 from Mycolicibacterium smegmatis MC2 155
MSMEG_4951 ribosomal protein L31 from Mycobacterium smegmatis str. MC2 155
38% identity, 93% 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> <sup>2</sup> 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...”
PMT1760 50S ribosomal protein L31 from Prochlorococcus marinus str. MIT 9313
29% identity, 83% coverage
ssl3445 50S ribosomal protein L31 from Synechocystis sp. PCC 6803
45% identity, 48% 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...”
SRIM_028075 50S ribosomal protein L31 from Streptomyces rimosus subsp. rimosus ATCC 10970
37% identity, 98% coverage
7nhk3 / A0A1B4XMV6 7nhk3 (see paper)
35% identity, 93% coverage
For advice on how to use these tools together, see
Interactive tools for functional annotation of bacterial genomes.
The PaperBLAST database links 793,807 different protein sequences to 1,259,118 scientific articles. Searches against EuropePMC were last performed on March 13 2025.
PaperBLAST builds a database of protein sequences that are linked
to scientific articles. These links come from automated text searches
against the articles in EuropePMC
and from manually-curated information from GeneRIF, UniProtKB/Swiss-Prot,
BRENDA,
CAZy (as made available by dbCAN),
BioLiP,
CharProtDB,
MetaCyc,
EcoCyc,
TCDB,
REBASE,
the Fitness Browser,
and a subset of the European Nucleotide Archive with the /experiment tag.
Given this database and a protein sequence query,
PaperBLAST uses protein-protein BLAST
to find similar sequences with E < 0.001.
To build the database, we query EuropePMC with locus tags, with RefSeq protein
identifiers, and with UniProt
accessions. We obtain the locus tags from RefSeq or from MicrobesOnline. We use
queries of the form "locus_tag AND genus_name" to try to ensure that
the paper is actually discussing that gene. Because EuropePMC indexes
most recent biomedical papers, even if they are not open access, some
of the links may be to papers that you cannot read or that our
computers cannot read. We query each of these identifiers that
appears in the open access part of EuropePMC, as well as every locus
tag that appears in the 500 most-referenced genomes, so that a gene
may appear in the PaperBLAST results even though none of the papers
that mention it are open access. We also incorporate text-mined links
from EuropePMC that link open access articles to UniProt or RefSeq
identifiers. (This yields some additional links because EuropePMC
uses different heuristics for their text mining than we do.)
For every article that mentions a locus tag, a RefSeq protein
identifier, or a UniProt accession, we try to select one or two
snippets of text that refer to the protein. If we cannot get access to
the full text, we try to select a snippet from the abstract, but
unfortunately, unique identifiers such as locus tags are rarely
provided in abstracts.
PaperBLAST also incorporates manually-curated protein functions:
- Proteins from NCBI's RefSeq are included if a
GeneRIF
entry links the gene to an article in
PubMed®.
GeneRIF also provides a short summary of the article's claim about the
protein, which is shown instead of a snippet.
- Proteins from Swiss-Prot (the curated part of UniProt)
are included if the curators
identified experimental evidence for the protein's function (evidence
code ECO:0000269). For these proteins, the fields of the Swiss-Prot entry that
describe the protein's function are shown (with bold headings).
- Proteins from BRENDA,
a curated database of enzymes, are included if they are linked to a paper in PubMed
and their full sequence is known.
- Every protein from the non-redundant subset of
BioLiP,
a database
of ligand-binding sites and catalytic residues in protein structures, is included. Since BioLiP itself
does not include descriptions of the proteins, those are taken from the
Protein Data Bank.
Descriptions from PDB rely on the original submitter of the
structure and cannot be updated by others, so they may be less reliable.
(For SitesBLAST and Sites on a Tree, we use a larger subset of BioLiP so that every
ligand is represented among a group of structures with similar sequences, but for
PaperBLAST, we use the non-redundant set provided by BioLiP.)
- Every protein from EcoCyc, a curated
database of the proteins in Escherichia coli K-12, is included, regardless
of whether they are characterized or not.
- Proteins from the MetaCyc metabolic pathway database
are included if they are linked to a paper in PubMed and their full sequence is known.
- Proteins from the Transport Classification Database (TCDB)
are included if they have known substrate(s), have reference(s),
and are not described as uncharacterized or putative.
(Some of the references are not visible on the PaperBLAST web site.)
- Every protein from CharProtDB,
a database of experimentally characterized protein annotations, is included.
- Proteins from the CAZy database of carbohydrate-active enzymes
are included if they are associated with an Enzyme Classification number.
Even though CAZy does not provide links from individual protein sequences to papers,
these should all be experimentally-characterized proteins.
- Proteins from the REBASE database
of restriction enzymes are included if they have known specificity.
- Every protein with an evidence-based reannotation (based on mutant phenotypes)
in the Fitness Browser is included.
- Sequence-specific transcription factors (including sigma factors and DNA-binding response regulators)
with experimentally-determined DNA binding sites from the
PRODORIC database of gene regulation in prokaryotes.
- Putative transcription factors from RegPrecise
that have manually-curated predictions for their binding sites. These predictions are based on
conserved putative regulatory sites across genomes that contain similar transcription factors,
so PaperBLAST clusters the TFs at 70% identity and retains just one member of each cluster.
- Coding sequence (CDS) features from the
European Nucleotide Archive (ENA)
are included if the /experiment tag is set (implying that there is experimental evidence for the annotation),
the nucleotide entry links to paper(s) in PubMed,
and the nucleotide entry is from the STD data class
(implying that these are targeted annotated sequences, not from shotgun sequencing).
Also, to filter out genes whose transcription or translation was detected, but whose function
was not studied, nucleotide entries or papers with more than 25 such proteins are excluded.
Descriptions from ENA rely on the original submitter of the
sequence and cannot be updated by others, so they may be less reliable.
Except for GeneRIF and ENA,
the curated entries include a short curated
description of the protein's function.
For entries from BioLiP, the protein's function may not be known beyond binding to the ligand.
Many of these entries also link to articles in PubMed.
For more information see the
PaperBLAST paper (mSystems 2017)
or the code.
You can download PaperBLAST's database here.
Changes to PaperBLAST since the paper was written:
- November 2023: incorporated PRODORIC and RegPrecise. Many PRODORIC entries were not linked to a protein sequence (no UniProt identifier), so we added this information.
- February 2023: BioLiP changed their download format. PaperBLAST now includes their non-redundant subset. SitesBLAST and Sites on a Tree use a larger non-redundant subset that ensures that every ligand is represented within each cluster. This should ensure that every binding site is represented.
- June 2022: incorporated some coding sequences from ENA with the /experiment tag.
- March 2022: incorporated BioLiP.
- April 2020: incorporated TCDB.
- April 2019: EuropePMC now returns table entries in their search results. This has expanded PaperBLAST's database, but most of the new entries are of low relevance, and the resulting snippets are often just lists of locus tags with annotations.
- February 2018: the alignment page reports the conservation of the hit's functional sites (if available from from Swiss-Prot or UniProt)
- January 2018: incorporated BRENDA.
- December 2017: incorporated MetaCyc, CharProtDB, CAZy, REBASE, and the reannotations from the Fitness Browser.
- September 2017: EuropePMC no longer returns some table entries in their search results. This has shrunk PaperBLAST's database, but has also reduced the number of low-relevance hits.
Many of these changes are described in Interactive tools for functional annotation of bacterial genomes.
PaperBLAST cannot provide snippets for many of the papers that are
published in non-open-access journals. This limitation applies even if
the paper is marked as "free" on the publisher's web site and is
available in PubmedCentral or EuropePMC. If a journal that you publish
in is marked as "secret," please consider publishing elsewhere.
Many important articles are missing from PaperBLAST, either because
the article's full text is not in EuropePMC (as for many older
articles), or because the paper does not mention a protein identifier such as a locus tag, or because of PaperBLAST's heuristics. If you notice an
article that characterizes a protein's function but is missing from
PaperBLAST, please notify the curators at UniProt
or add an entry to GeneRIF.
Entries in either of these databases will eventually be incorporated
into PaperBLAST. Note that to add an entry to UniProt, you will need
to find the UniProt identifier for the protein. If the protein is not
already in UniProt, you can ask them to create an entry. To add an
entry to GeneRIF, you will need an NCBI Gene identifier, but
unfortunately many prokaryotic proteins in RefSeq do not have
corresponding Gene identifers.
References
PaperBLAST: Text-mining papers for information about homologs.
M. N. Price and A. P. Arkin (2017). mSystems, 10.1128/mSystems.00039-17.
Europe PMC in 2017.
M. Levchenko et al (2017). Nucleic Acids Research, 10.1093/nar/gkx1005.
Gene indexing: characterization and analysis of NLM's GeneRIFs.
J. A. Mitchell et al (2003). AMIA Annu Symp Proc 2003:460-464.
UniProt: the universal protein knowledgebase.
The UniProt Consortium (2016). Nucleic Acids Research, 10.1093/nar/gkw1099.
BRENDA in 2017: new perspectives and new tools in BRENDA.
S. Placzek et al (2017). Nucleic Acids Research, 10.1093/nar/gkw952.
The EcoCyc database: reflecting new knowledge about Escherichia coli K-12.
I. M. Keeseler et al (2016). Nucleic Acids Research, 10.1093/nar/gkw1003.
The MetaCyc database of metabolic pathways and enzymes.
R. Caspi et al (2018). Nucleic Acids Research, 10.1093/nar/gkx935.
CharProtDB: a database of experimentally characterized protein annotations.
R. Madupu et al (2012). Nucleic Acids Research, 10.1093/nar/gkr1133.
The carbohydrate-active enzymes database (CAZy) in 2013.
V. Lombard et al (2014). Nucleic Acids Research, 10.1093/nar/gkt1178.
The Transporter Classification Database (TCDB): recent advances
M. H. Saier, Jr. et al (2016). Nucleic Acids Research, 10.1093/nar/gkv1103.
REBASE - a database for DNA restriction and modification: enzymes, genes and genomes.
R. J. Roberts et al (2015). Nucleic Acids Research, 10.1093/nar/gku1046.
Deep annotation of protein function across diverse bacteria from mutant phenotypes.
M. N. Price et al (2016). bioRxiv, 10.1101/072470.
by Morgan Price,
Arkin group
Lawrence Berkeley National Laboratory