Data files

Output files of phosphate probe binding on the surface of LDH from lactococcus lactis type 1. File with extension XPLOR can be visualized with a program VMD to identify the most favorable position for the phosphate binding. This relates to the Model "Part 4".

The Table represents the simulation results of how the presence of phosphate ions (Pi) in the solution might affect the activity of four LDH enzymes. This includes the algorithmic analysis of the binding energies values computed by the GRID program (see Part 4, model) for each enzyme in presence and absence of FBP molecule at pH 6 and 7. The analysis was performed by using the algorithm proposed in Part 5, model.

The file contains simulated data of the electron transport chain model (EcoliETC1) for varying parameter values, i.e. a local sensitivity analysis.

Excel sheet contains:

• flux distribution solution from best iteration cluster
• quality of the fit (experimental MIDs vs. simulated MIDs)
• Sensitivity analysis for 95% flux parameter confidence interval using a Monte-Carlo approach

Excel sheet contains:

• flux distribution solution from best iteration cluster
• quality of the fit (experimental MIDs vs. simulated MIDs)
• Sensitivity analysis for 95% flux parameter confidence interval using a Monte-Carlo approach

Excel sheet contains:

• flux distribution solution from best iteration cluster
• quality of the fit (experimental MIDs vs. simulated MIDs)
• Sensitivity analysis for 95% flux parameter confidence interval using a Monte-Carlo approach

Simulation results of PGK experimental data for ADP, ATP, 3PG and BPG saturation.

Simulation results of FBPAase of experimental data for DHAP and GAP saturation

Simulation results of GAPDH experimental data for BPG, NADPH, NADP, GAP, and Pi

Filtering of data in Perseus and t-test between conditions Perseus save file

Maxquant output.

Proteomics data comparing LXX cultures cultivated on mineral and in continuous culture: mineral samples: LNU-LXX9-Si00-14B-P-B-Pr LNU-LXX9-Si00-14B-P-C-Pr LNU-LXX9-Si00-14B-P-D-Pr conitnuous culture samples: LNU-LXX9-Si00-CnA-P-B2-Pr LNU-LXX9-Si00-CnA-P-B3-Pr LNU-LXX9-Si00-CnA-P-B4-Pr LNU-LXX9-Si00-CnA-P-B5-Pr LNU-LXX9-Si00-CnA-P-B6-Pr LNU-LXX9-Si00-CnA-P-B7-Pr

LFQ intensities from maxquant from combined search (mineral and continuous samples), filtered (at least 3 values in each condition), log-transformed

LFQ intensities from maxquant from combined search (mineral and continuous samples), log-transformed

Raw data and assembly for pacbio sequencing of L.ferriphilum.

Link to the repository for functional annotation

Genbank file for the L.ferriphilum chromosome, annotated with prokka 1.12beta

Table combining data for L.ferriphilum. RNAseq data, Proteomics LFQs, Functional annotation

Comparison between axenic and planktonic readcounts with deseq2

Comparison for LFQs with t-test in Perseus

Raw read files for samples

Normalized counts (tpm) for LF samples with mineral

Normalized counts (tpm) for L.ferriphilum samples from continuous culture.

Repository for omics data analysis