Model-driven Analysis

Introduction

In this document, we describe an Enzyme Constrained Model (ecModel) workflow for integrating absolute proteomics data (TMT-iBAQ) and analyzing metabolic modeling results from three S. cerevisiae strains: a Crabtree Positive, CENPK113-11C, used as reference; and two Crabtree Negative strains, sZJD23, and sZJD28.

Setup work-space

To run this pipeline the following packages are needed:

"tidyverse", "Metrics", "limma", "ggVennDiagram", "patchwork"

Data

For this analysis the following data is needed:

1. Fermentation data, as fluxes in Genome Scale Models are in [mmol/gDW/h], data are converted from [g/L] to [mmol/gDW/h]. For glucose, also [g/L] is keep since is required to determine yield.
2. Abundance proteomics, the dataset used here is in [fmol/ug Protein]
3. Total protein content in the cell, dataset is in [g/g Protein]

Prepare raw data

Proteomics

In GECKO v2 proteomics integration requires of protein usage (ub) to be in [mmol/gDW]. Then, if this version is used, we convert the data from [fmol/g] to [mmol/gDW].

Code

proteomics_v2 <- abundance |>
  replace_na(list(PrimaryGeneName = "unknown")) |> 
  rowwise() |>
  # 1. Converte to fmol/gDW.
  # 2. Convert fmol/ugDW to mmol/gDW. fmol = 10^-12 mmol, ugDW = 10^-6 gDW
  mutate(CENPK113_11C_1 = abundance_WT_1 * 1e-6 * prot_content$repl1[1],
         CENPK113_11C_2 = abundance_WT_2 * 1e-6 * prot_content$repl2[1],
         CENPK113_11C_3 = abundance_WT_3 * 1e-6 * prot_content$repl3[1],
         sZJD23_1 = abundance_sZJD23_1 * 1e-6 * prot_content$repl1[2],
         sZJD23_2 = abundance_sZJD23_2 * 1e-6 * prot_content$repl2[2],
         sZJD23_3 = abundance_sZJD23_3 * 1e-6 * prot_content$repl3[2],
         sZJD28_1 = abundance_sZJD28_1 * 1e-6 * prot_content$repl1[3],
         sZJD28_2 = abundance_sZJD28_2 * 1e-6 * prot_content$repl2[3],
         sZJD28_3 = abundance_sZJD28_3 * 1e-6 * prot_content$repl3[3]) |>
   select(1, 4, 29:37)

# Let's set some protein expression for PTA and PO values to zero in 11C
proteomics_v2[c(which(proteomics_v2$Accession == "Q8ZND6"),
            which(proteomics_v2$Accession == "D4YIP5")), 3:5] <- 0

# proteins 'P06169'=PDC1, 'P52910' = ACS2, and 'P41277' = GPP1 show expression
proteomics_v2[c(which(proteomics_v2$Accession == "P06169"),
            which(proteomics_v2$Accession == "P52910"),
            which(proteomics_v2$Accession == "P41277")), 6:11] <- 0

# add these proteins to set the model don't use these proteins
proteomics_v2 <- proteomics_v2 |>
  add_row(Accession = c("P16467", "P26263", "Q01574", "P40106"),
          GeneName = c("YLR134W", "YGR087C", "YAL054C", "YER062C"),
          CENPK113_11C_1 = rep(0, 4),
          CENPK113_11C_2 = rep(0, 4),
          CENPK113_11C_3 = rep(0, 4),
          sZJD23_1 = rep(0, 4),
          sZJD23_2 = rep(0, 4),
          sZJD23_3 = rep(0, 4),
          sZJD28_1 = rep(0, 4),
          sZJD28_2 = rep(0, 4),
          sZJD28_3 = rep(0, 4))

For GECKO v3 proteins usage needs to be in [mg/gDW]. Here, we will use GECKO v3, so let’s save this dataset in the data dir inside the predefined folder for GECKO.

Code

proteomics_v3 <- abundance |>
  rename(Entry = Accession) |>
  replace_na(list(PrimaryGeneName = "unknown")) |>
  rowwise() |>
  # 1. Converte to ug/gDW.
  # Convert fmol/ug -> mol/ug and Mw from kDa (kg/mol) -> ug/mol
  # Convert to mg/gDW
  mutate(CENPK113_11C_1 = 
           ((abundance_WT_1 * 10^-15) * (MW_kDa * 10^9)) * 
           prot_content$repl1[1] * 10^3,
         CENPK113_11C_2 = 
           ((abundance_WT_2 * 10^-15) * (MW_kDa * 10^9)) * 
           prot_content$repl2[1] * 10^3,
         CENPK113_11C_3 = 
           ((abundance_WT_3 * 10^-15) * (MW_kDa * 10^9)) * 
           prot_content$repl3[1] * 10^3,
         sZJD23_1 = 
           ((abundance_sZJD23_1 * 10^-15) * (MW_kDa * 10^9)) * 
           prot_content$repl1[2] * 10^3,
         sZJD23_2 = 
           ((abundance_sZJD23_2 * 10^-15) * (MW_kDa * 10^9)) * 
           prot_content$repl2[2] * 10^3,
         sZJD23_3 = 
           ((abundance_sZJD23_3 * 10^-15) * (MW_kDa * 10^9)) * 
           prot_content$repl3[2] * 10^3,
         sZJD28_1 = 
           ((abundance_sZJD28_1 * 10^-15) * (MW_kDa * 10^9)) * 
           prot_content$repl1[3] * 10^3,
         sZJD28_2 = 
           ((abundance_sZJD28_2 * 10^-15) * (MW_kDa * 10^9)) * 
           prot_content$repl2[3] * 10^3,
         sZJD28_3 = 
           ((abundance_sZJD28_3 * 10^-15) * (MW_kDa * 10^9)) * 
           prot_content$repl3[3] * 10^3) |>
  select(1, 29:37)

write_tsv(proteomics_v3,
          file = "../data/sceYeastGEM/data/proteomics.tsv",
          append = FALSE,
          col_names = TRUE)

Fermentation parameters

Other input required by GECKO is fermentation measurements in order to constraint the model. To do this, we need to change the concentrations from [g/L] to flux values [mmol/gDW/h]

First, let’s check the growth behavior over the time

Code

data_ferm |> 
  select(1:4) |> 
  filter(time < 50) |> 
  group_by(Name) |> 
  ggplot(aes(x = time,
             y = log(biomass),
             color = str_sub(Name, end = -3))) +
  geom_point() +
  scale_color_manual(values = color_strain) +
  facet_wrap(~Name, ncol = 3, scales = "free_x") +
  labs(x = "Time (h)",
       y = "log(Biomass [gDW/L])") +
  theme_minimal() +
  theme(legend.position = "none",
        text = element_text(size = 10))

log plots for exponential growth

Plot the growth curve for all the strains

Code

# Define a vector to scale the second axis
# 3.5 / 175, 6.25 / 125, 6.25 / 125
plots <- list()
sec_axis_val <- c(0.02, 0.05, 0.05)
min_x <- c(3, 8, 7)
max_x <- c(11.2, 40, 26)
# Remove some inconsistent data
filter_time <- c(12.5, 45, 40) 

for (i in 1:3) {
  plots[[i]] <- data_ferm |> 
    filter(str_starts(Name, condition[i])) |> 
    select(1:2, 4, 6:11) |> 
    rowwise() |> 
    mutate(biomass = biomass / sec_axis_val[i]) |>
    filter(time < filter_time[i]) |> 
    gather(variable, value, -time, -Name) |> 
    group_by(time, variable) |> 
    summarise(mean = mean(value), sd = sd(value)) |> 
    ggplot(aes(x = time, y = mean, color = variable)) +
    annotate(geom = "rect",
             xmin = min_x[i],
             xmax = max_x[i],
             ymin = 0,
             ymax = Inf,
             fill = "#79706E",
             alpha = 0.2) +
    geom_point(size = 2) +
    geom_smooth(se = FALSE, alpha = 0.7, linetype = 3) +
    geom_errorbar(aes(ymin = mean - sd, ymax = mean + sd),
                  colour = "black",
                  alpha = 0.5,
                  width = 0.2) +
    scale_y_continuous(sec.axis = sec_axis(~. * sec_axis_val[i],
                                           name = "[gDW/L]")) +
    scale_color_manual(values = color_ferm) +
    labs(x = "Time (h)", y = "[mmol/L]", colour = "") +
    theme_minimal() +
    theme(text = element_text(size = 10))

}

plots

[[1]]

CENPK113 11C

[[2]]

sZJD23

[[3]]

sZJD28

Code

rm(sec_axis_val, i, filter_time, plots)

Now, calculate the growth kinetics. Plotting the log of the biomass you can observe the start and end point of the exponential phase.

Code

ferm_params <- data.frame()

replicates <- data_ferm |> 
  distinct(Name) |> 
  pull()

min_x <- rep(min_x, each = 3)

max_x <-  rep(max_x, each = 3)

for (i in 1:length(replicates)) {
    tem_data <- data_ferm |> 
      filter((Name == replicates[i]) & between(time, min_x[i], max_x[i]))

    mu <- round(coefficients(lm(log(biomass) ~ time,
                                data = tem_data))[2], 3)

    yield <- round(coefficients(lm(biomass ~ glu_g,
                                   data = tem_data))[2], 3)

    rates <- coefficients(
      lm(cbind(glucose, ethanol, glycerol,
               acetate, pyruvate, succinate) ~ biomass,
         data = tem_data)) * mu

    params <- round(cbind(mu, yield, t(rates[-1, ])), 3)

    rownames(params) <- str_glue(replicates[i])

    ferm_params <- rbind(ferm_params, params)
}

rm(i, mu, yield, rates, params, tem_data, replicates)

ferm_params <- ferm_params |> 
  rownames_to_column() |> 
  rename(condition = rowname) |>
  add_column(ptot = as.numeric(c(prot_content[1, 2:4],
                                 prot_content[2, 2:4],
                                 prot_content[3, 2:4]))) |> 
  mutate(ptot = round(ptot, 3)) |> 
  add_column(co2 = c(25.649, 23.769, 21.061,
                     5.732, 5.277, 5.284,
                     6.787, 7.149, 6.157),
             oxygen = c(5.145, 5.774, 6.412,
                        4.792, 4.783, 4.852,
                        6.523, 6.048, 6.400))

Code

ferm_params |> 
  kbl() |> 
  kable_minimal() |> 
  scroll_box(width = "100%")

condition	mu	yield	glucose	ethanol	glycerol	acetate	pyruvate	succinate	ptot	co2	oxygen
CENPK113_11C_1	0.411	-0.147	-15.392	19.614	1.617	0.373	0.077	0.007	0.514	25.649	5.145
CENPK113_11C_2	0.422	-0.168	-13.845	19.283	0.721	0.582	0.108	0.008	0.541	23.769	5.774
CENPK113_11C_3	0.425	-0.169	-13.842	19.364	0.834	0.569	0.116	0.011	0.431	21.061	6.412
sZJD23_1	0.123	-0.269	-2.523	0.013	-0.001	1.077	0.037	0.039	0.402	5.732	4.792
sZJD23_2	0.124	-0.278	-2.448	0.000	0.002	0.967	0.033	0.031	0.428	5.277	4.783
sZJD23_3	0.134	-0.274	-2.690	0.006	0.003	1.144	0.046	0.039	0.332	5.284	4.852
sZJD28_1	0.167	-0.358	-2.578	0.000	0.000	0.450	0.000	0.000	0.416	6.787	6.523
sZJD28_2	0.180	-0.354	-2.796	-0.015	0.000	0.531	0.000	0.000	0.358	7.149	6.048
sZJD28_3	0.167	-0.417	-2.205	0.037	0.000	0.181	0.000	0.000	0.474	6.157	6.400

Finally, GECKO uses the average for each condition. Calculate them and export the file.

Enzyme Constrained Model

Enzyme constrained model simulations can be done with GECKO. Until here, we prepare all the input files needed for proteomics integrations. Nevertheless, GECKO runs in MATLAB. Code folder contains all the scripts to get an ecModel from an conventional one as well as the code for proteomics integration, and analysis of them.

To perform this section. Run:

1. get_ecModel.m to obtain the ecModel. Using GECKO v3 and modifying the model to incorporate those genes added by metabolic engineering (done by getAdaptedModel), and adjust some grRules identity in yeast-GEM to be critical and not consistent with information reported in Complex Portal (done by getUpdateModel). Here, we have previously create a folder in data named ecYeastGEM containing four subfolders code, data, models, output

2. test_ecModel.m to test the ecModel, this help to see if the ecModel have the ability to predict correctly the yeast behavior observed experimentally.

Next figures shows the behavior of the model compared to experimental data

Figure 1: Crabtree Effect

Figure 2: Growth rate by carbon source

3. integrate_proteomcis.m to constrain ecModel with proteomics data

4. analyze_prot_models.m once we have the protein models, constraint needs to be removed in order to see if the model is able to predict reasonably the behavior of the cell. This perform a series of FBA, FVA and calculate the enzyme usage.

After analysis, let´s visualize the variability in each protein model

Figure 3: Flux Variability Analysis

Analyse results from proteomics integration

Load the fermentation parameters from proteomics integration and take a look of the results. For that, plot the predicted fermentation parameters vs those observed experimentally

Code

pred_ferm_params <- read_tsv("../results/model_analysis/FBA/pred_ferm_params.txt",
                             col_names = TRUE,
                             show_col_types = FALSE) |> 
  rename(condition = Row) |> 
  mutate(across(where(is.numeric), round, 5))

pred_vs_exp <- pred_ferm_params |> 
  gather(variable, value, -condition) |> 
  inner_join(sum_ferm_params |> 
               gather(variable, value, -condition),
             by = c("condition", "variable"),
             suffix = c("_pred", "_exp")) |> 
  rename(predicted = value_pred,
         measured = value_exp) |> 
  mutate(variable = ifelse(variable != "co2", 
                           ifelse(variable == "grRate", 
                                  "Growth",
                                  str_to_title(variable)), 
                           str_to_upper(variable)),
         predicted = abs(predicted),
         error = abs(predicted-measured)/measured,
         error = replace_na(error, 0))

Code

pred_ferm_params |> 
  kbl() |> 
  kable_minimal() |> 
  scroll_box(width = "100%")

condition	grRate	glucose	co2	oxygen	acetate	ethanol	glycerol	pyruvate	succinate
CENPK113_11C	0.42004	-14.27599	23.49300	-5.70094	0.21738	17.5485	0	0.44294	0
sZJD23	0.12732	-2.43697	4.30975	-4.80900	0.00741	0.0000	0	1.60306	0
sZJD28	0.17143	-2.35855	4.49257	-4.39564	0.10693	0.0000	0	0.68514	0

Code

pred_vs_exp |> 
  ggplot(aes(x = measured,
             y = predicted,
             color = condition, 
             group = condition,
             shape = variable)) +
  geom_point(size = 4) +
  geom_abline(intercept = -0.1, slope = 0.95, linetype = "dashed") +
  annotate("text", 
           x = 2.5, 
           y = 20,
           hjust = 0,
           size = 3,
           label = str_glue("R^2: {r2} \n MAE: {mae}",
                            r2 = round(summary(
                              lm(predicted ~ measured, 
                                 pred_vs_exp))$adj.r.squared,
                              3),
                            mae = round(
                                    mae(pred_vs_exp$measured,
                                        predict(lm(predicted ~ measured, pred_vs_exp))), 3))) +
  scale_color_manual(values = color_strain) +
  scale_shape_manual(values = c(1:9)) +
  labs(x = "Measured",
       y = "Predicted",
       tag = "A.",
       caption = "Units: Growth Rate [1/h], Uptake and consumption rates [mmol/gDW/h]",
       color = "Strains",
       shape = "Parameter") +
  theme_minimal() +
  theme(plot.caption.position = "plot",
        plot.caption = element_text(hjust = 0),
        text = element_text(size = 10))

# Save the plot
p4_a <- last_plot() + theme(text = element_text(size = 8))

pred_vs_exp |> 
  ggplot(aes(x = error,
             y = variable, 
             color = condition)) +
  geom_point(size = 4, alpha = 0.5) +
  scale_color_manual(values = color_strain) +
  annotate(geom = "text",
           x = 30,
           y = 6.5,
           label = "PDH bypass",
           size = 3,
           lineheight = 0.9) +
  annotate( geom = "curve",
            x = 30, xend = 38,
            y = 6.8, yend = "Pyruvate",
            curvature = - 0.3,
            arrow = arrow(length = unit(0.25, "cm"))) +
  labs(x = "Relative error",
       y = "Parameter",
       tag = "B.",
       color = "Strains") +
  theme_minimal() +
  theme(plot.tag = element_text(face = "bold"),
        panel.spacing = unit(1, "lines"),
        strip.text = element_blank(),
        legend.margin = margin(t= -10),
        text = element_text(size = 10))
  
# Save the plot
p4_b <- last_plot() + theme(text = element_text(size = 8))

Fluxes

Error by parameter

Measured vs Predicted

Code

tibble(strain  = c("CENPK113_11C", "sZJD23", "sZJD28"),
       ptot = c(0.495, 0.387, 0.416),
       prot_measured = c(0.447, 0.360, 0.375),
       prot_model = c(0.239, 0.212, 0.236)) |> 
  gather(variable, value, -strain) |> 
  mutate(variable = factor(variable, 
                           levels = c("ptot", "prot_measured", "prot_model"))) |> 
  ggplot(aes(x = strain,
             y = value,
             label = str_glue("\n{value} g/gDW"),
             fill = variable)) +
  geom_col(position = "identity", alpha = 0.9) +
  scale_fill_manual(values = color_prot,
                    labels = c("Total", "Measured", "Model")) +
  geom_text(size = 2.25, vjust = 1.8, fontface = "bold") +
  labs(x = "", fill = "Protein content", tag = "C.") + 
  theme_minimal() +
  theme(plot.tag = element_text(face = "bold"),
        axis.line.y = element_blank(),
        axis.ticks.y = element_blank(),
        axis.text.y = element_blank(),
        axis.title.y = element_blank(),
        text = element_text(size = 10))

Code

# Save the plot
p4_c <- last_plot() + theme(text = element_text(size = 8))

Let’s look how each cell used enzymes (flux [ug/gDW]) and reactions per pathway (flux [mmol/gDW/h]). So, first let’s load the pathways in our model and download the pathways in Saccharomyces cerevisiae “sce” from KEGG

Code

pathways <- limma::getKEGGPathwayNames(species.KEGG = "sce", remove = TRUE)

gene_pathways <- limma::getGeneKEGGLinks(species.KEGG = "sce") |> 
  rename(GeneName = GeneID) |> 
  mutate(PathwayID = str_remove(PathwayID, "path:")) |> 
  add_row(GeneName = c("STM2338", "AWM76_03655"), 
          PathwayID = c("sce00620", "sce00620"))

pathway_level <- read_tsv("../data/pathway_level.txt",
                          show_col_types = FALSE,
                          col_names = TRUE) |> 
  inner_join(pathways, by = c("PathwayID", "Description")) |> 
  mutate(Description = case_when(
    (Description == "Valine, leucine and isoleucine degradation") ~ "Valine, leucine and isoleucine metabolism",
    (Description == "Valine, leucine and isoleucine biosynthesis") ~ "Valine, leucine and isoleucine metabolism",
    (Description == "Lysine biosynthesis") ~ "Lysine metabolism",
    (Description == "Lysine degradation") ~ "Lysine metabolism",
    .default = Description))

ecModel_pathways <- read_tsv("../data/ecModel_pathways.txt",
                             show_col_types = FALSE,
                             col_names = TRUE) |> 
  mutate(Description = case_when(
           (Description == "Glycolysis / gluconeogenesis") ~ "Glycolysis / Gluconeogenesis",
           (Description == "Pantothenate and coa biosynthesis") ~ "Pantothenate and CoA biosynthesis",
           (Description == "N-glycan biosynthesis") ~ "N-Glycan biosynthesis",
           .default = Description))

Code

data_fba <- list()

for (i in c("CENPK113_11C", "sZJD23", "sZJD28")) {
  data_fba[[i]] <- read_tsv(str_glue("../results/model_analysis/FBA/{i}.txt"),
                            col_names = c("rxnID", "rxnName", i),
                            show_col_types = FALSE,
                            skip = 1)
}

data_fba <- data_fba |> 
  # Create an unique dataframe with the flux data
  reduce(full_join,
         by = c("rxnID", "rxnName")) |> 
  mutate(across(CENPK113_11C:sZJD28, ~replace_na(., 0)),
         across(CENPK113_11C:sZJD28, abs)) |> 
  # Add pathways information
  left_join(ecModel_pathways, by = "rxnID") |> 
  # Add level to apply color in next plot
  left_join(pathway_level, by = "Description") |> 
  # Re order columns
  select(1, 2, 7:9, 6, 3:5) |> 
  mutate(across(level_1:PathwayID, ~replace_na(., "Other")))

Code

data_fba |> 
  mutate(CENPK113_11C_norm = abs(CENPK113_11C) / pred_ferm_params$grRate[[1]],
         sZJD23_norm = abs(sZJD23)  / pred_ferm_params$grRate[[2]],
         sZJD28_norm = abs(sZJD28)  / pred_ferm_params$grRate[[3]]) |> 
  gather(variable, value, -c(1:9)) |> 
  filter(value != 0) |> 
  # filter(level_2 != "Signal transduction") |> 
  ggplot(aes(x = log2(value), # str_remove(variable, "_norm")
             y = level_2,
             color = str_remove(variable, "_norm"))) +
  geom_boxplot(outlier.shape = 1, outlier.alpha = 0.5) +
  # geom_jitter(width = 0.1) +
  scale_color_manual(values = color_strain) +
  # geom_point(alpha = 0.4) +
  labs(x = "[mmol/gDW/h] (log transformed)",
       y = "Subsystem",
       color = "Strain") +
  theme_minimal() +
  theme(plot.tag = element_text(face = "bold"),
        legend.position = "bottom",
        text = element_text(size = 10))

Code

# Save the plot
p5 <- last_plot() + theme(text = element_text(size = 8))

Code

data_pca_fba <- data_fba |> 
  mutate(CENPK113_11C_norm = (CENPK113_11C / pred_ferm_params$grRate[[1]]),
         sZJD23_norm = (sZJD23  / pred_ferm_params$grRate[[2]]),
         sZJD28_norm = (sZJD28  / pred_ferm_params$grRate[[3]])) |> 
  filter(!str_starts(rxnID, "usage_prot")) |> 
  filter(rxnID != "prot_pool_exchange") |> 
  filter(Description != "Exchange reaction") |> 
  filter(!str_starts(Description, "Transport "))

pca_fba <- data_pca_fba |> 
  select(10:12) |> 
  prcomp()

# calculate the percentage for each PC
pca_fba$pct <- round(pca_fba$sdev^2 / sum(pca_fba$sdev^2) * 100, 3)

data_pca_fba |> 
  add_column(pca_fba$x |> as_tibble()) |> 
  filter(PC1 > 1) |> 
  ggplot(aes(x = PC1,
             y = PC2,
             color = level_2)) +
  geom_point() +
  geom_text_repel(aes(label = ifelse(PC1 > 2, rxnID, "")), size = 3) +
  geom_hline(yintercept = 0, linetype = 2, alpha = 0.5) +
  geom_vline(xintercept = 0, linetype = 2, alpha = 0.5) +
  scale_color_manual(values = c("#499894",
                                "#D37295", 
                                "#FF7F00", 
                                "#6A3D9A",
                                "#33A02C")) +
  labs(x = str_glue("PC1 ({pca_fba$pct[1]}%)"),
       y = str_glue("PC2 ({pca_fba$pct[2]}%)"),
       color = "Pathway") +
  theme_minimal()

Check those reactions with PC1 > 1

Code

data_pca_fba |> 
  add_column(pca_fba$x |> as_tibble()) |> 
  filter(PC1 > 1) |> 
  kbl() |> 
  kable_styling() |> 
  scroll_box(width = "100%", height = "50vh")

rxnID	rxnName	level_1	level_2	PathwayID	Description	CENPK113_11C	sZJD23	sZJD28	CENPK113_11C_norm	sZJD23_norm	sZJD28_norm	PC1	PC2	PC3
r_0091_EXP_2	(6-phosphogluconolactonase):	Metabolism	Carbohydrate metabolism	sce00030	Pentose phosphate pathway	3.19490	0.000000	0.398600	7.6061804	0.0000000	2.3251473	2.659481	5.5922943	-2.0590290
r_0148_EXP_2	(adenylate kinase):	Metabolism	Nucleotide metabolism	sce00230	Purine metabolism	3.14790	0.775150	1.010500	7.4942863	6.0882030	5.8945342	8.747495	2.0800893	-1.4111442
r_0226	(ATP synthase):	Metabolism	Energy metabolism	sce00190	Oxidative phosphorylation	11.21270	6.847600	10.444800	26.6943624	53.7825950	60.9274923	79.726892	-16.0925096	-18.8383165
r_0300_EXP_2	(citrate synthase):	Metabolism	Carbohydrate metabolism	sce00020	Citrate cycle (TCA cycle)	0.33111	0.979430	1.255300	0.7882821	7.6926642	7.3225223	7.338506	-4.8188561	-1.4680585
r_0303	(citrate to cis-aconitate(3-), cytoplasmic):	Metabolism	Carbohydrate metabolism	sce00020	Citrate cycle (TCA cycle)	0.58457	1.017400	1.060100	1.3917008	7.9908891	6.1838651	7.278931	-4.0627563	-0.3843812
r_0366_EXP_3	(enolase):	Metabolism	Carbohydrate metabolism	sce00010	Glycolysis / Gluconeogenesis	24.19960	3.882500	3.339300	57.6126083	30.4940308	19.4790877	57.454537	32.3456501	0.4995292
r_0438_EXP_2	(ferrocytochrome-c:oxygen oxidoreductase):	Metabolism	Energy metabolism	sce00190	Oxidative phosphorylation	21.31140	18.787900	16.979200	50.7365965	147.5644046	99.0445080	177.665322	-42.6150809	4.1960256
r_0439	(ubiquinol:ferricytochrome c reductase):	Metabolism	Energy metabolism	sce00190	Oxidative phosphorylation	10.65570	9.393900	8.489600	25.3682983	73.7818096	49.5222540	87.727711	-21.4787342	2.1088069
r_0450	(fructose-bisphosphate aldolase):	Metabolism	Carbohydrate metabolism	sce00010	Glycolysis / Gluconeogenesis	10.94560	1.955100	1.602900	26.0584706	15.3557964	9.3501721	26.166265	13.6795178	0.7097976
r_0466	(glucose 6-phosphate dehydrogenase):	Metabolism	Carbohydrate metabolism	sce00030	Pentose phosphate pathway	3.19490	0.177080	0.398600	7.6061804	1.3908263	2.3251473	3.656255	5.0585798	-1.2490984
r_0467	(glucose-6-phosphate isomerase):	Metabolism	Carbohydrate metabolism	sce00010	Glycolysis / Gluconeogenesis	10.39010	2.050400	1.677900	24.7359775	16.1043041	9.7876684	26.275774	12.1060736	0.8235335
r_0471_EXP_2	(glutamate dehydrogenase (NADP)):	Metabolism	Amino acid metabolism	sce00250	Alanine, aspartate and glutamate metabolism	4.11670	0.741090	0.895600	9.8007333	5.8206880	5.2242898	9.346583	4.3978978	-1.0804658
r_0486_EXP_1	(glyceraldehyde-3-phosphate dehydrogenase):	Metabolism	Carbohydrate metabolism	sce00010	Glycolysis / Gluconeogenesis	18.05150	4.017900	2.228000	42.9756690	31.5574929	12.9965584	47.846356	21.1232244	6.7552584
r_0486_EXP_2	(glyceraldehyde-3-phosphate dehydrogenase):	Metabolism	Carbohydrate metabolism	sce00010	Glycolysis / Gluconeogenesis	6.78900	0.000000	1.276200	16.1627464	0.0000000	7.4444380	9.384686	11.5125273	-6.4344618
r_0534_EXP_2	(hexokinase (D-glucose:ATP)):	Metabolism	Carbohydrate metabolism	sce00010	Glycolysis / Gluconeogenesis	0.94259	0.108610	1.946400	2.2440482	0.8530474	11.3539054	5.156334	-2.1417258	-8.7634515
r_0534_EXP_3	(hexokinase (D-glucose:ATP)):	Metabolism	Carbohydrate metabolism	sce00010	Glycolysis / Gluconeogenesis	0.43039	2.328400	0.412100	1.0246405	18.2877788	2.4038966	12.595175	-7.1924893	8.6925762
r_0534_EXP_4	(hexokinase (D-glucose:ATP)):	Metabolism	Carbohydrate metabolism	sce00010	Glycolysis / Gluconeogenesis	5.84980	0.000000	0.000000	13.9267689	0.0000000	0.0000000	4.583147	11.8102433	-0.3290675
r_0534_EXP_5	(hexokinase (D-glucose:ATP)):	Metabolism	Carbohydrate metabolism	sce00010	Glycolysis / Gluconeogenesis	7.05320	0.000000	0.000000	16.7917341	0.0000000	0.0000000	5.980473	14.3103012	-0.4012972
r_0569	(inorganic diphosphatase):	Metabolism	Energy metabolism	sce00190	Oxidative phosphorylation	1.42940	1.151500	0.434430	3.4030092	9.0441407	2.5341539	7.195396	-1.6092540	3.1438537
r_0659	(isocitrate dehydrogenase (NADP)):	Metabolism	Carbohydrate metabolism	sce00020	Citrate cycle (TCA cycle)	0.58457	1.017400	1.060100	1.3917008	7.9908891	6.1838651	7.278931	-4.0627563	-0.3843812
r_0713	(malate dehydrogenase):	Metabolism	Carbohydrate metabolism	sce00020	Citrate cycle (TCA cycle)	0.58457	1.883800	1.255300	1.3917008	14.7957901	7.3225223	12.723463	-7.0180420	2.6531468
r_0714_REV	(malate dehydrogenase, cytoplasmic (reversible)):	Metabolism	Carbohydrate metabolism	sce00020	Citrate cycle (TCA cycle)	0.34487	0.675840	0.140750	0.8210409	5.3081998	0.8210348	2.404655	-1.9112148	2.4253743
r_0770_EXP_1	(NADH dehydrogenase, cytosolic/mitochondrial):	Metabolism	Energy metabolism	sce00190	Oxidative phosphorylation	1.97980	1.039600	0.000000	4.7133606	8.1652529	0.0000000	5.941359	0.6370088	4.6581501
r_0770_EXP_2	(NADH dehydrogenase, cytosolic/mitochondrial):	Metabolism	Energy metabolism	sce00190	Oxidative phosphorylation	5.74310	4.112700	3.583300	13.6727455	32.3020735	20.9024091	38.029102	-7.1214322	1.5036767
r_0773	(NADH:ubiquinone oxidoreductase):	Metabolism	Energy metabolism	sce00190	Oxidative phosphorylation	2.71780	2.507500	3.845800	6.4703362	19.6944706	22.4336464	26.244001	-9.0310208	-6.9008395
r_0886	(phosphofructokinase):	Metabolism	Carbohydrate metabolism	sce00010	Glycolysis / Gluconeogenesis	10.94560	1.955100	1.602900	26.0584706	15.3557964	9.3501721	26.166265	13.6795178	0.7097976
r_0889_EXP_2	(phosphogluconate dehydrogenase):	Metabolism	Carbohydrate metabolism	sce00030	Pentose phosphate pathway	3.19490	0.008378	0.345300	7.6061804	0.0658027	2.0142332	2.551652	5.6609677	-1.7680745
r_0892	(phosphoglycerate kinase):	Metabolism	Carbohydrate metabolism	sce00010	Glycolysis / Gluconeogenesis	24.84050	4.012800	3.504200	59.1384154	31.5174364	20.4409963	59.411672	32.9938118	0.2754247
r_0893_EXP_2	(phosphoglycerate mutase):	Metabolism	Carbohydrate metabolism	sce00010	Glycolysis / Gluconeogenesis	24.19960	3.882500	3.339300	57.6126083	30.4940308	19.4790877	57.454537	32.3456501	0.4995292
r_0958_EXP_1	(pyruvate carboxylase):	Metabolism	Carbohydrate metabolism	sce00620	Pyruvate metabolism	0.96768	0.293310	0.394920	2.3037806	2.3037229	2.3036808	1.713674	0.0877112	-0.5663607
r_0959_EXP_2	(pyruvate decarboxylase):	Metabolism	Carbohydrate metabolism	sce00010	Glycolysis / Gluconeogenesis	17.54850	0.000000	0.000000	41.7781640	0.0000000	0.0000000	18.167072	36.1142379	-1.0312394
r_0961	(pyruvate dehydrogenase):	Metabolism	Carbohydrate metabolism	sce00010	Glycolysis / Gluconeogenesis	1.92790	1.482200	1.515800	4.5898010	11.6415331	8.8420930	12.780176	-3.4759171	-0.4990607
r_0962_EXP_1	(pyruvate kinase):	Metabolism	Carbohydrate metabolism	sce00010	Glycolysis / Gluconeogenesis	23.84640	3.251100	2.572400	56.7717360	25.5348728	15.0055416	51.260277	34.8663212	1.2678303
r_1021_EXP_2	(succinate dehydrogenase (ubiquinone-6)):	Metabolism	Carbohydrate metabolism	sce00020	Citrate cycle (TCA cycle)	0.21498	1.734100	1.060500	0.5118084	13.6200126	6.1861984	10.885213	-6.9913980	2.9139572
r_1022	(succinate-CoA ligase (ADP-forming)):	Metabolism	Carbohydrate metabolism	sce00020	Citrate cycle (TCA cycle)	0.78341	1.135300	1.113700	1.8650843	8.9169023	6.4965292	8.329327	-4.0994678	-0.1111205
r_1054	(triose-phosphate isomerase):	Metabolism	Carbohydrate metabolism	sce00010	Glycolysis / Gluconeogenesis	11.94720	1.994900	1.709900	28.4430054	15.6683946	9.9743335	27.864442	15.4518272	0.3245519
r_1667	(bicarbonate formation):	Metabolism	Energy metabolism	sce00910	Nitrogen metabolism	1.58760	0.481200	0.647920	3.7796400	3.7794533	3.7795018	4.226801	0.3634639	-0.9433828
r_2115_EXP_2	(alcohol dehydrogenase, (acetaldehyde to ethanol)):	Metabolism	Carbohydrate metabolism	sce00010	Glycolysis / Gluconeogenesis	17.54850	0.000000	0.000000	41.7781640	0.0000000	0.0000000	18.167072	36.1142379	-1.0312394
r_2305	(cis-aconitate(3-) to isocitrate):	Metabolism	Carbohydrate metabolism	sce00020	Citrate cycle (TCA cycle)	0.58457	1.017400	1.060100	1.3917008	7.9908891	6.1838651	7.278931	-4.0627563	-0.3843812
r_4046	(non-growth associated maintenance reaction):	Other	Other	Other	Growth	0.70000	0.700000	0.700000	1.6665080	5.4979579	4.0832993	4.579220	-2.2317531	-0.1362102
r_4226_REV	(L-Alanine:2-oxoglutarate aminotransferase (reversible)):	Metabolism	Amino acid metabolism	sce00250	Alanine, aspartate and glutamate metabolism	2.41300	0.052239	0.070337	5.7446910	0.4102969	0.4102957	1.091093	4.3889136	-0.2172429
r_4264	(succinate:NAD+ oxidoreductase):	Other	Other	Other	Cellular response to anaerobic conditions	0.16483	0.572540	0.000000	0.3924150	4.4968583	0.0000000	1.204853	-1.7258761	2.6308425
r_0163	(alcohol dehydrogenase (ethanol to acetaldehyde)):	Metabolism	Carbohydrate metabolism	sce00010	Glycolysis / Gluconeogenesis	0.00000	1.619700	0.000000	0.0000000	12.7214892	0.0000000	6.907870	-5.2244228	7.4302487
r_0165_EXP_2	(mitochondrial alcohol dehydrogenase):	Metabolism	Carbohydrate metabolism	sce00010	Glycolysis / Gluconeogenesis	0.00000	1.619700	0.000000	0.0000000	12.7214892	0.0000000	6.907870	-5.2244228	7.4302487
r_0217	(aspartate transaminase):	Metabolism	Amino acid metabolism	sce00250	Alanine, aspartate and glutamate metabolism	0.00000	0.571310	0.000000	0.0000000	4.4871976	0.0000000	1.006537	-2.0646024	2.6351100
r_0451	(fumarase):	Metabolism	Carbohydrate metabolism	sce00020	Citrate cycle (TCA cycle)	0.00000	1.135300	1.016800	0.0000000	8.9169023	5.9312839	7.137902	-5.5562428	0.3951943
r_0505_EXP_2	(glycine-cleavage complex (lipoamide)):	Metabolism	Amino acid metabolism	sce00260	Glycine, serine and threonine metabolism	0.00000	1.135300	1.016800	0.0000000	8.9169023	5.9312839	7.137902	-5.5562428	0.3951943
r_0831_EXP_1	(oxoglutarate dehydrogenase (dihydrolipoamide S-succinyltransferase)):	Metabolism	Carbohydrate metabolism	sce00020	Citrate cycle (TCA cycle)	0.00000	1.135300	0.000000	0.0000000	8.9169023	0.0000000	4.181208	-3.7644537	5.2146942
r_0832_EXP_1	(oxoglutarate dehydrogenase (lipoamide)):	Metabolism	Carbohydrate metabolism	sce00020	Citrate cycle (TCA cycle)	0.00000	1.135300	0.000000	0.0000000	8.9169023	0.0000000	4.181208	-3.7644537	5.2146942
r_0962_EXP_2	(pyruvate kinase):	Metabolism	Carbohydrate metabolism	sce00010	Glycolysis / Gluconeogenesis	0.00000	0.524350	0.622770	0.0000000	4.1183632	3.6327947	2.553119	-3.0205017	-0.5315251

Load the enzyme usage for each random solution and calculate the average and standard deviation

Code

enz_usage <- list()

for (i in condition) {
  enz_usage[[i]] <- read_tsv(
    str_glue("../results/model_analysis/enzUsage/enzUsage_{i}.txt"),
    col_names = c("protID",
                  str_glue("LB_{i}"), 
                  str_glue("absUsage_{i}"), 
                  str_glue("capUsage_{i}")),
    show_col_types = FALSE,
    skip = 1)
}

enz_usage <- enz_usage |> 
  reduce(full_join,
         by = "protID") |> 
  mutate(across(LB_CENPK113_11C:capUsage_sZJD28, ~replace_na(.,0)),
         across(LB_CENPK113_11C:capUsage_sZJD28, abs)) |> 
  inner_join(abundance |> 
               rename(protID = Accession) |> 
               select(protID, PrimaryGeneName, GeneName),
             by = "protID") |> 
  select(1, 11, 12, 2:10)

Code

enz_usage |> 
  # Add KEGG pathway information for each gene 
  left_join(gene_pathways, by = "GeneName", multiple = "all") |> 
  left_join(pathway_level, by = "PathwayID") |> 
  relocate(PathwayID:Description, .after = GeneName) |> 
  mutate(across(PathwayID:Description, ~replace_na(., "Other"))) |> 
  select(1:7, starts_with("absUsage_")) |> 
  gather(variable, value, -c(1:7)) |> 
  filter(level_2 != "Global and overview maps" & value != 0) |> 
  mutate(variable = str_remove(variable, "absUsage_"),
         value = case_when(
           (variable == "CENPK113_11C") ~ value / pred_ferm_params$grRate[[1]],
           (variable == "sZJD23") ~ value / pred_ferm_params$grRate[[2]],
           (variable == "sZJD28") ~ value / pred_ferm_params$grRate[[3]])) |> 
  mutate(variable = str_remove(variable, "absUsage_")) |> 
  group_by(level_2, variable) |> 
  summarise(usage = sum(value) / 1000) |> 
  ggplot(aes(x = usage, y = level_2, fill = variable)) +
  geom_col(position = "dodge", alpha = 0.8) +
  scale_fill_manual(values = color_strain) +
  labs(x = "Protein usage [g/gDW] / [1/h]", 
       y = "Subsystem",
       fill = "Strain") +
  theme_minimal()

Code

# Save the plot
p6 <- last_plot() + theme(text = element_text(size = 8))

Code

enz_usage |> 
  # Add KEGG pathway information for each gene 
  left_join(gene_pathways, by = "GeneName", multiple = "all") |> 
  left_join(pathway_level, by = "PathwayID") |> 
  relocate(PathwayID:Description, .after = GeneName) |> 
  mutate(across(PathwayID:Description, ~replace_na(., "Other"))) |> 
  select(1:7, starts_with("absUsage_")) |> 
  gather(variable, value, -c(1:7)) |> 
  filter(level_2 != "Global and overview maps" & value != 0) |> 
  mutate(variable = str_remove(variable, "absUsage_"),
         value = case_when(
           (variable == "CENPK113_11C") ~ value / pred_ferm_params$grRate[[1]],
           (variable == "sZJD23") ~ value / pred_ferm_params$grRate[[2]],
           (variable == "sZJD28") ~ value / pred_ferm_params$grRate[[3]])) |> 
  group_by(Description, variable) |> 
  summarise(usage = sum(value) / 1000) |> 
  ggplot(aes(x = usage, y = Description, fill = variable)) +
  geom_col(position = "dodge", alpha = 0.8) +
  scale_fill_manual(values = color_strain) +
  labs(x = "Protein usage [g/gDW/h]", 
       y = "Subsystem",
       fill = "Strain") +
  theme_minimal()

Some protein have high usage, usually reaching the UB. Let’s compared those protein and the reactions associated to those. Here, we identified a highUsage protein when UB/flux is higher than 0.75

Code

high_usage <- list()

for (i in condition) {
  high_usage[[i]] <- read_tsv(
    str_glue("../results/model_analysis/enzUsage/highUsage_{i}.txt"),
    show_col_types = FALSE,
    col_names = TRUE) |> 
    left_join(enz_usage |> select(protID, PrimaryGeneName), by = "protID") |> 
    relocate(PrimaryGeneName, .after = protID)
}

venn_data <- process_data(Venn(list(high_usage[["CENPK113_11C"]] |> 
                                      distinct(protID) |> 
                                      select(protID) |>
                                      pull(),
                                    high_usage[["sZJD23"]] |> 
                                      distinct(protID) |> 
                                      select(protID) |> 
                                      pull(),
                                    high_usage[["sZJD28"]] |> 
                                      distinct(protID) |> 
                                      select(protID) |> 
                                      pull())))

Code

ggplot() +
  # 1. region count layer
  geom_sf(aes(fill = name), 
          data = venn_region(venn_data), 
          alpha = 0.8) +
  # 2. set edge layer
  geom_sf(aes(color = id), 
          data = venn_setedge(venn_data),
          show.legend = FALSE) +
  # 3. region label layer
  geom_sf_text(aes(label = 
                     str_glue("{count} \n {percent}%",
                              percent = 
                                round((count * 100) / 
                                        sum(venn_data@region[["count"]]), 1))),
               data = venn_region(venn_data),
               size = 2) +
  scale_fill_manual(values = color_set,
                    breaks = c("Set_1", "Set_2", "Set_3"),
                    labels = c("Set_1" = "CENPK113_11C",
                               "Set_2" = "sZJD23",
                               "Set_3" = "sZJD28")) +
  scale_color_manual(values = c("#5A5A5A","#003F88", "#FFB703")) +
  scale_x_continuous(expand = expansion(mult = .2)) +
  labs(tag = "A.",
       fill = "Strain") +
  theme_void() + 
  theme(plot.tag = element_text(face = "bold"))

Code

# Save the plot
p7_a <- last_plot() + theme(text = element_text(size = 8))

Code

process_region_data(
  Venn(list(high_usage[["CENPK113_11C"]] |> 
                     distinct(PrimaryGeneName) |> 
                     select(PrimaryGeneName) |>
                     pull(),
                   high_usage[["sZJD23"]] |> 
                     distinct(PrimaryGeneName) |> 
                     select(PrimaryGeneName) |> 
                     pull(),
                   high_usage[["sZJD28"]] |> 
                     distinct(PrimaryGeneName) |> 
                     select(PrimaryGeneName) |> 
                     pull()))) |> 
  mutate(name = str_replace(name, "Set_1", "CENPK113 11C"),
         name = str_replace(name, "Set_2", "sZJD23"),
         name = str_replace(name, "Set_3", "sZJD28")) |> 
  kbl() |> 
  kable_styling()

component	id	item	count	name
region	1	ACC1 , ARG8 , TRP3 , ERG27, FBA1 , PMT4 , TDH1 , SHM1 , HXK2 , BNA2 , MET16, PFK1 , PFK2 , PRS3 , PDX3 , RKI1 , ERG6 , TRR1 , YPQ1 , SAM3 , FAS1 , FAS2 , ZRC1	23	CENPK113 11C
region	2	DPS1 , COX13, PRO1 , GLN4 , KGD2 , LSC2 , SDH2 , SDH1 , PIC2 , TAM41, ATM1	11	sZJD23
region	3	SPXB , FAA2 , LYS20, LSC1 , MVD1 , BNA6 , ERG1 , DIP5 , AGP2 , PTR2	10	sZJD28
region	12	ILV6 , CIT3 , ARG5,6, ATP1 , ATP2 , ATP18 , COX5A , HXK1 , NDE1 , THS1 , TPO4 , PNS1	12	CENPK113 11C..sZJD23
region	13	KRE6 , ADE6 , ERG20 , QCR7 , RIP1 , GLK1 , BNA4 , ALT1 , MCT1 , unknown, TKL2 , HXT2 , HXT3 , LYP1	14	CENPK113 11C..sZJD28
region	23	GSC2 , ATP17, COX2 , KGD1 , HMG2 , IDP2 , GND2 , PDB1 , LAT1 , PYK2 , VBA1 , GPT2 , IRC24, LIP5 , ALG5 , HPA3	16	sZJD23..sZJD28
region	123	FKS1 , PUT2 , ILV2 , LEU1 , LYS4 , MRI1 , ACH1 , PDH1 , ADK1 , ADE13, TRP4 , ASN2 , ATP3 , ATP5 , ATP7 , ATP4 , ATP20, BIO2 , ERG25, ERG4 , ARO2 , CYS3 , URA4 , PMT1 , COR1 , QCR10, QCR2 , MIS1 , GUS1 , TDH3 , GUT2 , LPD1 , GRS1 , GUA1 , LYS21, ERG13, ADE17, IDI1 , LAP2 , SAM2 , MES1 , QNS1 , NDI1 , URA5 , PCM1 , SEC53, SER1 , PDA1 , PDX1 , YCF1 , RNR1 , SES1 , TRP5 , QRI1 , UGP1 , PUS1 , ODC2 , FCY2 , AAC3 , YHM2 , CAN1 , AVT3 , MUP1 , OAC1 , PHO91, MIR1 , YMC1 , TSC13, OLE1 , FAA1 , FAA4 , CDS1 , PSD1 , NEO1 , NFS1 , ADP1 , SPF1 , COT1 , DUG1 , STT3 , FRE1 , ALG9 , ALG12, CTS1 , ZRT1	85	CENPK113 11C..sZJD23..sZJD28

Enhancing cell growth

Proteomics integration allow to understand the metabolism under certain conditions. PDH bypass integrated in sZJD23 have show to allow growth at high glucose concentrations without alcohol production and subsequently reverse engineering in sZJD28 have show improve the growth rate. Nevertheless, compared to other natural crabtree negative microorganisms sZJD23 growth slow. A proposal to improve cell growth by using ecModels is understanding the protein requirements.

Code

enzUsage_by_grRate <- list()

grRates <- seq(0.05, 0.4, by = 0.05)

for (i in grRates) {
  enzUsage_by_grRate[[as.character(i)]] <- read_tsv(
    str_glue("../results/model_analysis/enhancing_growth/enzUsage_{i}.txt"),
    col_names = c("protID",
                  str_glue("LB_{i}"), 
                  str_glue("absUsage_{i}"), 
                  str_glue("capUsage_{i}")),
    show_col_types = FALSE,
    skip = 1)
}

enzUsage_by_grRate <- enzUsage_by_grRate |> 
  reduce(full_join,
         by = "protID") |> 
  select(1, starts_with("absUsage_")) |> 
  mutate(across(absUsage_0.05:absUsage_0.4, abs)) |> 
  inner_join(abundance |> 
               rename(protID = Accession) |> 
               select(protID, PrimaryGeneName, GeneName),
             by = "protID") |> 
  relocate(GeneName, PrimaryGeneName, .after = protID) |> 
  left_join(gene_pathways, by = "GeneName", multiple = "all") |> 
  left_join(pathway_level, by = "PathwayID") |> 
  relocate(PathwayID:Description, .after = GeneName) |> 
  mutate(across(PathwayID:Description, ~replace_na(., "Other"))) |> 
  left_join(enz_usage |> select(protID, absUsage_sZJD28), by = "protID")

Take a look of the results. Firstly, visualize the distribution of protein usage for POav and PTAse compared to proteomics data and protein model for sZJD28 to determine if the area limiting step to reach higher growth rates as natural crabtree microorganism

Code

enzUsage_by_grRate |> 
  filter(protID == "D4YIP5" | protID == "Q8ZND6") |> 
  gather(variable, value, -c(1:7)) |> 
  filter(value != 0 & variable != "absUsage_sZJD28") |> 
  mutate(variable = as.double(str_remove(variable, "absUsage_"))) |> 
  ggplot(aes(x = variable,
             y = value, 
             group = protID, 
             color = protID)) +
  geom_point(size = 3) +
  geom_smooth(method = "lm", se = FALSE) +
  geom_hline(yintercept = enz_usage |> 
               filter(protID == "D4YIP5") |> 
               select(absUsage_sZJD28) |> 
               pull(), 
             linetype = 2, 
             alpha = 0.5) +
  geom_hline(yintercept = enz_usage |> 
               filter(protID == "Q8ZND6") |> 
               select(absUsage_sZJD28) |> 
               pull(), 
             linetype = 2, 
             alpha = 0.5) +
  geom_vline(xintercept = pred_ferm_params$grRate[[3]], 
             linetype = 2, 
             alpha = 0.5) +
  geom_hline(yintercept = 0.552, linetype = 2, color = "#E31A1C", alpha = 0.5) +
  # geom_hline(yintercept = 8.543455, linetype = 2, color = "#E31A1C", alpha = 0.5) +
  annotate(geom = "text",
           x = 0.19,
           y = 2.4,
           label = str_glue("\u00b5 sZJD28"),
           size = 2,
           hjust = -0.1,
           lineheight = 0.9) +
  annotate(geom = "text",
           x = 0.1,
           y = enz_usage |> 
               filter(protID == "D4YIP5") |> 
               select(absUsage_sZJD28) |> 
               pull(),
           label = " POav usage - ecModel sZJD28",
           size = 2,
           hjust = -0.1,
           vjust = -1,
           lineheight = 0.9) +
  annotate(geom = "text",
           x = 0.3,
           y = 0.552,
           label = "Proteomics limit POav",
           size = 2,
           hjust = 1,
           vjust = 1.2,
           lineheight = 0.9) +
  annotate(geom = "text",
           x = 0.1,
           y = enz_usage |> 
               filter(protID == "Q8ZND6") |> 
               select(absUsage_sZJD28) |> 
               pull(),
           label = " PTAse usage - ecModel sZJD28",
           size = 2,
           hjust = -0.1,
           vjust = -1,
           lineheight = 0.9) +
  annotate(geom = "segment",
           x = 0.172, xend = 0.19,
           y = 2.4, yend = 2.4,
           arrow = arrow(length = unit(0.25, "cm"))) +
  scale_color_manual(values = c("#FF7F00", "#33A02C"),
                     labels = c("POav", "PTAse")) +
  labs(x = "Growth rate [1/h]",
       y = "Protein usage [mg/gDW]",
       color = "",
       tag = "B.",
       caption = str_glue("Piruvate Oxidase in proteomcis: 0.552 [g/gDW]\n",
                          "Phosphate acetyltransferase in proteomcis: 8.544 [g/gDW]")) +
  theme_minimal() +
  theme(plot.tag = element_text(face = "bold"))

Code

# Save the plot
p7_b <- last_plot() + theme(text = element_text(size = 8))

Take a look of the results. First, visualize the distribution of protein usage of engineering yeast strain without proteomics constraint aiming to identify potential bottlenecks to reach highest growth rates, similar to those found in nature

Code

enzUsage_by_grRate |> 
  gather(variable, value, -c(1:7)) |> 
  filter(level_2 != "Global and overview maps" & value != 0) |> 
  mutate(variable = str_remove(variable, "absUsage_"),
         value = case_when(
           (variable == "0.05") ~ value / 0.05,
           (variable == "0.1") ~ value / 0.1,
           (variable == "0.15") ~ value / 0.15,
           (variable == "0.2") ~ value / 0.2,
           (variable == "0.25") ~ value / 0.25,
           (variable == "0.3") ~ value / 0.3,
           (variable == "0.35") ~ value / 0.35,
           (variable == "0.4") ~ value / 0.4,
           (variable == "sZJD28") ~ value / pred_ferm_params$grRate[[3]])) |> 
  group_by(level_2, variable) |> 
  summarise(usage = sum(value) / 1000) |> 
  ggplot(aes(x = usage, y = level_2, fill = variable)) +
  geom_col(position = "dodge", alpha = 0.8) +
  scale_fill_manual(values = c("#FDBF6F",
                               "#B2DF8A",
                               "#CAB2D6",
                               "#9D7660",
                               "#499894",
                               "#33A02C",
                               "#FF7F00",
                               "#6A3D9A",
                               "#D37295",
                               "#FFB703")) +
  labs(x = "Protein usage [g/gDW] / Growth rate", 
       y = "Subsystem",
       fill = "Growth rate",
       caption = "") +
  theme_minimal()

Code

enzUsage_by_grRate |> 
  gather(variable, value, -c(1:7)) |> 
  filter(level_2 != "Global and overview maps" & value != 0) |> 
  mutate(variable = str_remove(variable, "absUsage_")) |> 
  group_by(level_2, variable) |> 
  summarise(usage = sum(value) / 1000) |> 
  ggplot(aes(x = usage, y = level_2, fill = variable)) +
  geom_col(position = "dodge", alpha = 0.8) +
  scale_fill_manual(values = c("#FDBF6F",
                               "#B2DF8A",
                               "#CAB2D6",
                               "#9D7660",
                               "#499894",
                               "#33A02C",
                               "#FF7F00",
                               "#6A3D9A",
                               "#D37295",
                               "#FFB703")) +
  labs(x = "Protein usage [g/gDW]", 
       y = "Subsystem",
       fill = "Growth Rate",
       caption = "Growth rate sZJD28: 0.171 [1/h]") +
  theme_minimal()

Code

FVA_neg <- read_tsv("../results/model_analysis/enhancing_growth/FVA_ecModel_neg.txt",
                    show_col_types = FALSE, 
                    col_names = TRUE)

FVA_ko_GPD1 <- read_tsv("../results/model_analysis/enhancing_growth/FVA_ko_GPD1.txt",
                        show_col_types = FALSE, 
                        col_names = TRUE)

FVA_neg |> 
  inner_join(FVA_ko_GPD1, 
             by = c("rxnId", "rxnName"),
             suffix = c("_neg", "_ko")) |> 
  mutate(var_neg = maxFluxes_neg - minFluxes_neg,
         var_ko = maxFluxes_ko - minFluxes_ko,
         changes = var_neg - var_ko) |> 
  filter(changes != 0) |> 
  filter(str_starts(rxnId, "usage_prot_")) |> 
  arrange(desc(changes)) |> 
  kbl() |> 
  kable_styling() |> 
  scroll_box(width = "100%", height = "50vh")

rxnId	rxnName	minFluxes_neg	maxFluxes_neg	minFluxes_ko	maxFluxes_ko	var_neg	var_ko	changes
usage_prot_P32191	usage_prot_P32191	-48.9328409	0.0000000	-0.7106583	0.0000000	48.9328409	0.7106583	48.2221826
usage_prot_Q00055	usage_prot_Q00055	-0.8372521	0.0000000	0.0000000	0.0000000	0.8372521	0.0000000	0.8372521
usage_prot_P14065	usage_prot_P14065	-8.8425664	0.0000000	-8.8160654	0.0000000	8.8425664	8.8160654	0.0265010
usage_prot_P36035	usage_prot_P36035	-61.5603552	0.0000000	-61.5376816	0.0000000	61.5603552	61.5376816	0.0226736
usage_prot_P00359	usage_prot_P00359	-60.9713002	0.0000000	-60.9502625	0.0000000	60.9713002	60.9502625	0.0210377
usage_prot_P00360	usage_prot_P00360	-60.9713002	0.0000000	-60.9502625	0.0000000	60.9713002	60.9502625	0.0210377
usage_prot_P14540	usage_prot_P14540	-59.8500393	0.0000000	-59.8298103	0.0000000	59.8500393	59.8298103	0.0202290
usage_prot_P54862	usage_prot_P54862	-59.4619404	0.0000000	-59.4427768	0.0000000	59.4619404	59.4427768	0.0191636
usage_prot_P39924	usage_prot_P39924	-59.4619404	0.0000000	-59.4427768	0.0000000	59.4619404	59.4427768	0.0191636
usage_prot_P23585	usage_prot_P23585	-59.4619404	0.0000000	-59.4427768	0.0000000	59.4619404	59.4427768	0.0191636
usage_prot_P32467	usage_prot_P32467	-59.4619404	0.0000000	-59.4427768	0.0000000	59.4619404	59.4427768	0.0191636
usage_prot_P32465	usage_prot_P32465	-59.4619404	0.0000000	-59.4427768	0.0000000	59.4619404	59.4427768	0.0191636
usage_prot_P39003	usage_prot_P39003	-59.4619404	0.0000000	-59.4427768	0.0000000	59.4619404	59.4427768	0.0191636
usage_prot_P32466	usage_prot_P32466	-59.4619404	0.0000000	-59.4427768	0.0000000	59.4619404	59.4427768	0.0191636
usage_prot_P40886	usage_prot_P40886	-59.4619404	0.0000000	-59.4427768	0.0000000	59.4619404	59.4427768	0.0191636
usage_prot_P40885	usage_prot_P40885	-59.4619404	0.0000000	-59.4427768	0.0000000	59.4619404	59.4427768	0.0191636
usage_prot_P38695	usage_prot_P38695	-59.4619404	0.0000000	-59.4427768	0.0000000	59.4619404	59.4427768	0.0191636
usage_prot_P47185	usage_prot_P47185	-59.4619404	0.0000000	-59.4427768	0.0000000	59.4619404	59.4427768	0.0191636
usage_prot_P53631	usage_prot_P53631	-59.4619404	0.0000000	-59.4427768	0.0000000	59.4619404	59.4427768	0.0191636
usage_prot_P39004	usage_prot_P39004	-59.4619404	0.0000000	-59.4427768	0.0000000	59.4619404	59.4427768	0.0191636
usage_prot_P43581	usage_prot_P43581	-59.4619404	0.0000000	-59.4427768	0.0000000	59.4619404	59.4427768	0.0191636
usage_prot_P54854	usage_prot_P54854	-59.4619404	0.0000000	-59.4427768	0.0000000	59.4619404	59.4427768	0.0191636
usage_prot_P0CX11	usage_prot_P0CX11	-59.1712373	0.0000000	-59.1520854	0.0000000	59.1712373	59.1520854	0.0191519
usage_prot_P42222	usage_prot_P42222	-59.1712373	0.0000000	-59.1520854	0.0000000	59.1712373	59.1520854	0.0191519
usage_prot_P0CX10	usage_prot_P0CX10	-59.1712373	0.0000000	-59.1520854	0.0000000	59.1712373	59.1520854	0.0191519
usage_prot_P00925	usage_prot_P00925	-59.1712373	0.0000000	-59.1520854	0.0000000	59.1712373	59.1520854	0.0191519
usage_prot_P00924	usage_prot_P00924	-59.1712373	0.0000000	-59.1520854	0.0000000	59.1712373	59.1520854	0.0191519
usage_prot_P0CD90	usage_prot_P0CD90	-63.0960964	0.0000000	-63.0770234	0.0000000	63.0960964	63.0770234	0.0190730
usage_prot_P0CD91	usage_prot_P0CD91	-63.0960964	0.0000000	-63.0770234	0.0000000	63.0960964	63.0770234	0.0190730
usage_prot_P00560	usage_prot_P00560	-59.0462071	0.0000000	-59.0271967	0.0000000	59.0462071	59.0271967	0.0190105
usage_prot_Q12040	usage_prot_Q12040	-58.9145842	0.0000000	-58.8957098	0.0000000	58.9145842	58.8957098	0.0188744
usage_prot_Q06204	usage_prot_Q06204	-54.6694355	0.0000000	-54.6506253	0.0000000	54.6694355	54.6506253	0.0188102
usage_prot_P19358	usage_prot_P19358	-58.8267021	0.0000000	-58.8079231	0.0000000	58.8267021	58.8079231	0.0187790
usage_prot_P20051	usage_prot_P20051	-58.9086495	-0.0823401	-58.8898706	-0.0823401	58.8263094	58.8075305	0.0187789
usage_prot_P39518	usage_prot_P39518	-58.8263094	0.0000000	-58.8075305	0.0000000	58.8263094	58.8075305	0.0187789
usage_prot_Q12209	usage_prot_Q12209	-58.8263094	0.0000000	-58.8075305	0.0000000	58.8263094	58.8075305	0.0187789
usage_prot_Q08986	usage_prot_Q08986	-58.8263094	0.0000000	-58.8075305	0.0000000	58.8263094	58.8075305	0.0187789
usage_prot_Q05788	usage_prot_Q05788	-58.8263094	0.0000000	-58.8075305	0.0000000	58.8263094	58.8075305	0.0187789
usage_prot_Q07830	usage_prot_Q07830	-58.8263094	0.0000000	-58.8075305	0.0000000	58.8263094	58.8075305	0.0187789
usage_prot_P53228	usage_prot_P53228	-58.8263094	0.0000000	-58.8075305	0.0000000	58.8263094	58.8075305	0.0187789
usage_prot_Q12436	usage_prot_Q12436	-58.8264412	0.0000000	-58.8076623	0.0000000	58.8264412	58.8076623	0.0187789
usage_prot_P22133	usage_prot_P22133	-58.8264631	0.0000000	-58.8076842	0.0000000	58.8264631	58.8076842	0.0187789
usage_prot_P38773	usage_prot_P38773	-58.8263094	0.0000000	-58.8075305	0.0000000	58.8263094	58.8075305	0.0187789
usage_prot_P38774	usage_prot_P38774	-58.8263094	0.0000000	-58.8075305	0.0000000	58.8263094	58.8075305	0.0187789
usage_prot_P32804	usage_prot_P32804	-58.8264412	0.0000000	-58.8076623	0.0000000	58.8264412	58.8076623	0.0187789
usage_prot_P38361	usage_prot_P38361	-59.1824060	0.0000000	-59.1636271	0.0000000	59.1824060	59.1636271	0.0187789
usage_prot_P40054	usage_prot_P40054	-58.8498517	0.0000000	-58.8310728	0.0000000	58.8498517	58.8310728	0.0187789
usage_prot_P38152	usage_prot_P38152	-58.8450994	0.0000000	-58.8263205	0.0000000	58.8450994	58.8263205	0.0187789
usage_prot_P15380	usage_prot_P15380	-58.8263725	0.0000000	-58.8075936	0.0000000	58.8263725	58.8075936	0.0187789
usage_prot_P38702	usage_prot_P38702	-58.8444414	0.0000000	-58.8256625	0.0000000	58.8444414	58.8256625	0.0187789
usage_prot_P53388	usage_prot_P53388	-58.8263725	0.0000000	-58.8075936	0.0000000	58.8263725	58.8075936	0.0187789
usage_prot_P41815	usage_prot_P41815	-58.8263094	0.0000000	-58.8075305	0.0000000	58.8263094	58.8075305	0.0187789
usage_prot_P0CH63	usage_prot_P0CH63	-58.8263094	0.0000000	-58.8075305	0.0000000	58.8263094	58.8075305	0.0187789
usage_prot_P0CH64	usage_prot_P0CH64	-58.8263094	0.0000000	-58.8075305	0.0000000	58.8263094	58.8075305	0.0187789
usage_prot_P40510	usage_prot_P40510	-58.8498517	0.0000000	-58.8310728	0.0000000	58.8498517	58.8310728	0.0187789
usage_prot_P32487	usage_prot_P32487	-58.8263094	0.0000000	-58.8075305	0.0000000	58.8263094	58.8075305	0.0187789
usage_prot_P43623	usage_prot_P43623	-58.8263094	0.0000000	-58.8075305	0.0000000	58.8263094	58.8075305	0.0187789
usage_prot_P48567	usage_prot_P48567	-58.8263094	0.0000000	-58.8075305	0.0000000	58.8263094	58.8075305	0.0187789
usage_prot_P31373	usage_prot_P31373	-58.8277691	0.0000000	-58.8089902	0.0000000	58.8277691	58.8089902	0.0187789
usage_prot_Q12674	usage_prot_Q12674	-58.8263094	0.0000000	-58.8075305	0.0000000	58.8263094	58.8075305	0.0187789
usage_prot_Q08645	usage_prot_Q08645	-58.8263094	0.0000000	-58.8075305	0.0000000	58.8263094	58.8075305	0.0187789
usage_prot_P38709	usage_prot_P38709	-58.8687127	0.0000000	-58.8499338	0.0000000	58.8687127	58.8499338	0.0187789
usage_prot_Q12211	usage_prot_Q12211	-58.8263094	0.0000000	-58.8075305	0.0000000	58.8263094	58.8075305	0.0187789
usage_prot_Q04533	usage_prot_Q04533	-58.8292288	0.0000000	-58.8104499	0.0000000	58.8292288	58.8104499	0.0187789
usage_prot_Q03175	usage_prot_Q03175	-58.8263094	0.0000000	-58.8075305	0.0000000	58.8263094	58.8075305	0.0187789
usage_prot_P25612	usage_prot_P25612	-58.8263094	0.0000000	-58.8075305	0.0000000	58.8263094	58.8075305	0.0187789
usage_prot_P38967	usage_prot_P38967	-58.8263725	0.0000000	-58.8075936	0.0000000	58.8263725	58.8075936	0.0187789
usage_prot_Q04806	usage_prot_Q04806	-58.8263094	0.0000000	-58.8075305	0.0000000	58.8263094	58.8075305	0.0187789
usage_prot_Q12412	usage_prot_Q12412	-58.8263094	0.0000000	-58.8075305	0.0000000	58.8263094	58.8075305	0.0187789
usage_prot_P32331	usage_prot_P32331	-58.8268936	0.0000000	-58.8081147	0.0000000	58.8268936	58.8081147	0.0187789
usage_prot_P40857	usage_prot_P40857	-58.8263094	0.0000000	-58.8075305	0.0000000	58.8263094	58.8075305	0.0187789
usage_prot_P36051	usage_prot_P36051	-58.8263094	0.0000000	-58.8075305	0.0000000	58.8263094	58.8075305	0.0187789
usage_prot_Q02896	usage_prot_Q02896	-58.8263094	0.0000000	-58.8075305	0.0000000	58.8263094	58.8075305	0.0187789
usage_prot_P38818	usage_prot_P38818	-58.8263094	0.0000000	-58.8075305	0.0000000	58.8263094	58.8075305	0.0187789
usage_prot_P26364	usage_prot_P26364	-58.8263094	0.0000000	-58.8075305	0.0000000	58.8263094	58.8075305	0.0187789
usage_prot_P47176	usage_prot_P47176	-58.8278785	-0.0011640	-58.8090996	-0.0011640	58.8267145	58.8079356	0.0187789
usage_prot_P54113	usage_prot_P54113	-59.0335774	0.0000000	-59.0147985	0.0000000	59.0335774	59.0147985	0.0187789
usage_prot_P15700	usage_prot_P15700	-58.8266024	-0.0002923	-58.8078235	-0.0002923	58.8263100	58.8075311	0.0187789
usage_prot_P38925	usage_prot_P38925	-58.8265443	-0.0002349	-58.8077654	-0.0002349	58.8263094	58.8075305	0.0187789
usage_prot_P23542	usage_prot_P23542	-58.8319277	0.0000000	-58.8131488	0.0000000	58.8319277	58.8131488	0.0187789
usage_prot_P32463	usage_prot_P32463	-58.8263094	0.0000000	-58.8075305	0.0000000	58.8263094	58.8075305	0.0187789
usage_prot_P47164	usage_prot_P47164	-58.8294135	0.0000000	-58.8106346	0.0000000	58.8294135	58.8106346	0.0187789
usage_prot_P33413	usage_prot_P33413	-58.8263094	0.0000000	-58.8075305	0.0000000	58.8263094	58.8075305	0.0187789
usage_prot_P10356	usage_prot_P10356	-58.8268143	0.0000000	-58.8080354	0.0000000	58.8268143	58.8080354	0.0187789
usage_prot_P04817	usage_prot_P04817	-58.8263094	0.0000000	-58.8075305	0.0000000	58.8263094	58.8075305	0.0187789
usage_prot_P40029	usage_prot_P40029	-58.8263094	0.0000000	-58.8075305	0.0000000	58.8263094	58.8075305	0.0187789
usage_prot_Q12358	usage_prot_Q12358	-58.8263094	0.0000000	-58.8075305	0.0000000	58.8263094	58.8075305	0.0187789
usage_prot_P47039	usage_prot_P47039	-58.8268143	0.0000000	-58.8080354	0.0000000	58.8268143	58.8080354	0.0187789
usage_prot_Q06510	usage_prot_Q06510	-58.8263094	0.0000000	-58.8075305	0.0000000	58.8263094	58.8075305	0.0187789
usage_prot_P09440	usage_prot_P09440	-58.8263223	0.0000000	-58.8075434	0.0000000	58.8263223	58.8075434	0.0187789
usage_prot_Q08742	usage_prot_Q08742	-58.8263094	0.0000000	-58.8075305	0.0000000	58.8263094	58.8075305	0.0187789
usage_prot_P38795	usage_prot_P38795	-58.8957869	-0.0694775	-58.8770080	-0.0694775	58.8263094	58.8075305	0.0187789
usage_prot_P0CX09	usage_prot_P0CX09	-58.8263094	0.0000000	-58.8075305	0.0000000	58.8263094	58.8075305	0.0187789
usage_prot_Q01662	usage_prot_Q01662	-58.8263094	0.0000000	-58.8075305	0.0000000	58.8263094	58.8075305	0.0187789
usage_prot_P06775	usage_prot_P06775	-58.8266570	0.0000000	-58.8078781	0.0000000	58.8266570	58.8078781	0.0187789
usage_prot_P53090	usage_prot_P53090	-58.8283208	0.0000000	-58.8095418	0.0000000	58.8283208	58.8095418	0.0187789
usage_prot_P40107	usage_prot_P40107	-58.8263138	0.0000000	-58.8075349	0.0000000	58.8263138	58.8075349	0.0187789
usage_prot_Q04013	usage_prot_Q04013	-58.8967977	0.0000000	-58.8780188	0.0000000	58.8967977	58.8780188	0.0187789
usage_prot_Q08908	usage_prot_Q08908	-58.8263094	0.0000000	-58.8075305	0.0000000	58.8263094	58.8075305	0.0187789
usage_prot_P32419	usage_prot_P32419	-58.8263094	0.0000000	-58.8075305	0.0000000	58.8263094	58.8075305	0.0187789
usage_prot_P47119	usage_prot_P47119	-58.8263290	0.0000000	-58.8075500	0.0000000	58.8263290	58.8075500	0.0187789
usage_prot_P41948	usage_prot_P41948	-59.7360970	0.0000000	-59.7173181	0.0000000	59.7360970	59.7173181	0.0187789
usage_prot_Q08409	usage_prot_Q08409	-58.8263094	0.0000000	-58.8075305	0.0000000	58.8263094	58.8075305	0.0187789
usage_prot_P50276	usage_prot_P50276	-58.8263094	0.0000000	-58.8075305	0.0000000	58.8263094	58.8075305	0.0187789
usage_prot_P13298	usage_prot_P13298	-58.8378774	0.0000000	-58.8190985	0.0000000	58.8378774	58.8190985	0.0187789
usage_prot_P53746	usage_prot_P53746	-58.8263094	0.0000000	-58.8075305	0.0000000	58.8263094	58.8075305	0.0187789
usage_prot_P25376	usage_prot_P25376	-58.8263725	0.0000000	-58.8075936	0.0000000	58.8263725	58.8075936	0.0187789
usage_prot_P40260	usage_prot_P40260	-59.7360970	0.0000000	-59.7173181	0.0000000	59.7360970	59.7173181	0.0187789
usage_prot_P22580	usage_prot_P22580	-58.8263094	0.0000000	-58.8075305	0.0000000	58.8263094	58.8075305	0.0187789
usage_prot_P49367	usage_prot_P49367	-59.2944112	-0.4666682	-59.2756323	-0.4666682	58.8277430	58.8089640	0.0187789
usage_prot_P40544	usage_prot_P40544	-58.8263094	0.0000000	-58.8075305	0.0000000	58.8263094	58.8075305	0.0187789
usage_prot_P53167	usage_prot_P53167	-58.8263094	0.0000000	-58.8075305	0.0000000	58.8263094	58.8075305	0.0187789
usage_prot_P53099	usage_prot_P53099	-58.8263094	0.0000000	-58.8075305	0.0000000	58.8263094	58.8075305	0.0187789
usage_prot_Q04089	usage_prot_Q04089	-58.8263094	0.0000000	-58.8075305	0.0000000	58.8263094	58.8075305	0.0187789
usage_prot_Q03786	usage_prot_Q03786	-58.8263094	0.0000000	-58.8075305	0.0000000	58.8263094	58.8075305	0.0187789
usage_prot_Q99297	usage_prot_Q99297	-58.9409230	0.0000000	-58.9221441	0.0000000	58.9409230	58.9221441	0.0187789
usage_prot_P07245	usage_prot_P07245	-58.9552284	-0.0027937	-58.9364495	-0.0027937	58.9524347	58.9336558	0.0187789
usage_prot_P49954	usage_prot_P49954	-58.8263094	0.0000000	-58.8075305	0.0000000	58.8263094	58.8075305	0.0187789
usage_prot_P39714	usage_prot_P39714	-58.8263094	0.0000000	-58.8075305	0.0000000	58.8263094	58.8075305	0.0187789
usage_prot_P38971	usage_prot_P38971	-58.8263094	0.0000000	-58.8075305	0.0000000	58.8263094	58.8075305	0.0187789
usage_prot_Q08361	usage_prot_Q08361	-58.8263094	0.0000000	-58.8075305	0.0000000	58.8263094	58.8075305	0.0187789
usage_prot_Q06350	usage_prot_Q06350	-58.8263094	0.0000000	-58.8075305	0.0000000	58.8263094	58.8075305	0.0187789
usage_prot_Q08905	usage_prot_Q08905	-58.8263094	0.0000000	-58.8075305	0.0000000	58.8263094	58.8075305	0.0187789
usage_prot_P47912	usage_prot_P47912	-58.8305006	0.0000000	-58.8117216	0.0000000	58.8305006	58.8117216	0.0187789
usage_prot_P14772	usage_prot_P14772	-58.8263094	0.0000000	-58.8075305	0.0000000	58.8263094	58.8075305	0.0187789
usage_prot_P38137	usage_prot_P38137	-58.8263094	0.0000000	-58.8075305	0.0000000	58.8263094	58.8075305	0.0187789
usage_prot_P38084	usage_prot_P38084	-58.8263094	0.0000000	-58.8075305	0.0000000	58.8263094	58.8075305	0.0187789
usage_prot_Q04121	usage_prot_Q04121	-58.8285687	0.0000000	-58.8097898	0.0000000	58.8285687	58.8097898	0.0187789
usage_prot_P0CX08	usage_prot_P0CX08	-58.8263094	0.0000000	-58.8075305	0.0000000	58.8263094	58.8075305	0.0187789
usage_prot_Q12333	usage_prot_Q12333	-58.8263094	0.0000000	-58.8075305	0.0000000	58.8263094	58.8075305	0.0187789
usage_prot_P39002	usage_prot_P39002	-58.8263094	0.0000000	-58.8075305	0.0000000	58.8263094	58.8075305	0.0187789
usage_prot_Q06489	usage_prot_Q06489	-58.8264212	-0.0001118	-58.8076423	-0.0001118	58.8263094	58.8075305	0.0187789
usage_prot_P38734	usage_prot_P38734	-58.8263094	0.0000000	-58.8075305	0.0000000	58.8263094	58.8075305	0.0187789
usage_prot_P52893	usage_prot_P52893	-58.8263094	0.0000000	-58.8075305	0.0000000	58.8263094	58.8075305	0.0187789
usage_prot_P39533	usage_prot_P39533	-58.8716271	0.0000000	-58.8528481	0.0000000	58.8716271	58.8528481	0.0187789
usage_prot_Q08914	usage_prot_Q08914	-58.8263094	0.0000000	-58.8075305	0.0000000	58.8263094	58.8075305	0.0187789
usage_prot_P38211	usage_prot_P38211	-58.8263094	0.0000000	-58.8075305	0.0000000	58.8263094	58.8075305	0.0187789
usage_prot_P46367	usage_prot_P46367	-58.8263094	0.0000000	-58.8075305	0.0000000	58.8263094	58.8075305	0.0187789
usage_prot_P47182	usage_prot_P47182	-58.8263094	0.0000000	-58.8075305	0.0000000	58.8263094	58.8075305	0.0187789
usage_prot_P38085	usage_prot_P38085	-58.8263094	0.0000000	-58.8075305	0.0000000	58.8263094	58.8075305	0.0187789
usage_prot_P38329	usage_prot_P38329	-58.8263094	0.0000000	-58.8075305	0.0000000	58.8263094	58.8075305	0.0187789
usage_prot_P07283	usage_prot_P07283	-60.0089850	-1.1826756	-59.9902061	-1.1826756	58.8263094	58.8075305	0.0187789
usage_prot_Q05016	usage_prot_Q05016	-58.8263094	0.0000000	-58.8075305	0.0000000	58.8263094	58.8075305	0.0187789
usage_prot_P17064	usage_prot_P17064	-58.8263094	0.0000000	-58.8075305	0.0000000	58.8263094	58.8075305	0.0187789
usage_prot_P53839	usage_prot_P53839	-58.8263094	0.0000000	-58.8075305	0.0000000	58.8263094	58.8075305	0.0187789
usage_prot_P32791	usage_prot_P32791	-58.8263094	0.0000000	-58.8075305	0.0000000	58.8263094	58.8075305	0.0187789
usage_prot_P32451	usage_prot_P32451	-58.8263094	0.0000000	-58.8075305	0.0000000	58.8263094	58.8075305	0.0187789
usage_prot_P53283	usage_prot_P53283	-58.8263094	0.0000000	-58.8075305	0.0000000	58.8263094	58.8075305	0.0187789
usage_prot_P43548	usage_prot_P43548	-58.8263094	0.0000000	-58.8075305	0.0000000	58.8263094	58.8075305	0.0187789
usage_prot_P49775	usage_prot_P49775	-58.8263094	0.0000000	-58.8075305	0.0000000	58.8263094	58.8075305	0.0187789
usage_prot_Q12305	usage_prot_Q12305	-58.8263094	0.0000000	-58.8075305	0.0000000	58.8263094	58.8075305	0.0187789
usage_prot_Q12359	usage_prot_Q12359	-59.7360970	0.0000000	-59.7173181	0.0000000	59.7360970	59.7173181	0.0187789
usage_prot_Q04728	usage_prot_Q04728	-58.8462660	-0.0199566	-58.8274871	-0.0199566	58.8263094	58.8075305	0.0187789
usage_prot_P23900	usage_prot_P23900	-58.8263094	0.0000000	-58.8075305	0.0000000	58.8263094	58.8075305	0.0187789
usage_prot_P36001	usage_prot_P36001	-58.8263094	0.0000000	-58.8075305	0.0000000	58.8263094	58.8075305	0.0187789
usage_prot_Q02891	usage_prot_Q02891	-58.8263094	0.0000000	-58.8075305	0.0000000	58.8263094	58.8075305	0.0187789
usage_prot_P38174	usage_prot_P38174	-58.8263094	0.0000000	-58.8075305	0.0000000	58.8263094	58.8075305	0.0187789
usage_prot_P32861	usage_prot_P32861	-58.8687127	0.0000000	-58.8499338	0.0000000	58.8687127	58.8499338	0.0187789
usage_prot_P53230	usage_prot_P53230	-58.8263094	0.0000000	-58.8075305	0.0000000	58.8263094	58.8075305	0.0187789
usage_prot_P53223	usage_prot_P53223	-58.8263094	0.0000000	-58.8075305	0.0000000	58.8263094	58.8075305	0.0187789
usage_prot_Q03028	usage_prot_Q03028	-58.9409230	0.0000000	-58.9221441	0.0000000	58.9409230	58.9221441	0.0187789
usage_prot_P43545	usage_prot_P43545	-58.8263094	0.0000000	-58.8075305	0.0000000	58.8263094	58.8075305	0.0187789
usage_prot_P07275	usage_prot_P07275	-59.5050621	0.0000000	-59.4862832	0.0000000	59.5050621	59.4862832	0.0187789
usage_prot_P43636	usage_prot_P43636	-58.8263094	0.0000000	-58.8075305	0.0000000	58.8263094	58.8075305	0.0187789
usage_prot_P39524	usage_prot_P39524	-58.8263094	0.0000000	-58.8075305	0.0000000	58.8263094	58.8075305	0.0187789
usage_prot_P30624	usage_prot_P30624	-58.8305006	0.0000000	-58.8117216	0.0000000	58.8305006	58.8117216	0.0187789
usage_prot_P36033	usage_prot_P36033	-58.8263094	0.0000000	-58.8075305	0.0000000	58.8263094	58.8075305	0.0187789
usage_prot_Q06328	usage_prot_Q06328	-58.8263094	0.0000000	-58.8075305	0.0000000	58.8263094	58.8075305	0.0187789
usage_prot_Q12119	usage_prot_Q12119	-58.8263094	0.0000000	-58.8075305	0.0000000	58.8263094	58.8075305	0.0187789
usage_prot_Q01976	usage_prot_Q01976	-58.8263094	0.0000000	-58.8075305	0.0000000	58.8263094	58.8075305	0.0187789
usage_prot_P39535	usage_prot_P39535	-59.1824060	0.0000000	-59.1636271	0.0000000	59.1824060	59.1636271	0.0187789
usage_prot_P53824	usage_prot_P53824	-58.8263094	0.0000000	-58.8075305	0.0000000	58.8263094	58.8075305	0.0187789
usage_prot_Q04458	usage_prot_Q04458	-58.8263168	0.0000000	-58.8075379	0.0000000	58.8263168	58.8075379	0.0187789
usage_prot_P37291	usage_prot_P37291	-58.9161672	0.0000000	-58.8973883	0.0000000	58.9161672	58.8973883	0.0187789
usage_prot_P43123	usage_prot_P43123	-58.8263094	0.0000000	-58.8075305	0.0000000	58.8263094	58.8075305	0.0187789
usage_prot_Q12251	usage_prot_Q12251	-58.8263094	0.0000000	-58.8075305	0.0000000	58.8263094	58.8075305	0.0187789
usage_prot_P38009	usage_prot_P38009	-59.0335774	0.0000000	-59.0147985	0.0000000	59.0335774	59.0147985	0.0187789
usage_prot_P30777	usage_prot_P30777	-58.8263094	0.0000000	-58.8075305	0.0000000	58.8263094	58.8075305	0.0187789
usage_prot_Q04299	usage_prot_Q04299	-58.8263094	0.0000000	-58.8075305	0.0000000	58.8263094	58.8075305	0.0187789
usage_prot_P53206	usage_prot_P53206	-58.8263094	0.0000000	-58.8075305	0.0000000	58.8263094	58.8075305	0.0187789
usage_prot_P40580	usage_prot_P40580	-58.8263094	0.0000000	-58.8075305	0.0000000	58.8263094	58.8075305	0.0187789
usage_prot_P20107	usage_prot_P20107	-58.8263094	0.0000000	-58.8075305	0.0000000	58.8263094	58.8075305	0.0187789
usage_prot_P38840	usage_prot_P38840	-58.8272548	0.0000000	-58.8084759	0.0000000	58.8272548	58.8084759	0.0187789
usage_prot_P40416	usage_prot_P40416	-58.8263094	0.0000000	-58.8075305	0.0000000	58.8263094	58.8075305	0.0187789
usage_prot_P32316	usage_prot_P32316	-58.8263094	0.0000000	-58.8075305	0.0000000	58.8263094	58.8075305	0.0187789
usage_prot_P47016	usage_prot_P47016	-58.8263094	0.0000000	-58.8075305	0.0000000	58.8263094	58.8075305	0.0187789
usage_prot_P47026	usage_prot_P47026	-58.8263094	0.0000000	-58.8075305	0.0000000	58.8263094	58.8075305	0.0187789
usage_prot_P38226	usage_prot_P38226	-58.8263094	0.0000000	-58.8075305	0.0000000	58.8263094	58.8075305	0.0187789
usage_prot_Q06508	usage_prot_Q06508	-58.8263094	0.0000000	-58.8075305	0.0000000	58.8263094	58.8075305	0.0187789
usage_prot_P38230	usage_prot_P38230	-58.8263094	0.0000000	-58.8075305	0.0000000	58.8263094	58.8075305	0.0187789
usage_prot_P25346	usage_prot_P25346	-58.8263094	0.0000000	-58.8075305	0.0000000	58.8263094	58.8075305	0.0187789
usage_prot_Q07747	usage_prot_Q07747	-58.8263094	0.0000000	-58.8075305	0.0000000	58.8263094	58.8075305	0.0187789
usage_prot_P29952	usage_prot_P29952	-58.8377833	-0.0114738	-58.8190043	-0.0114738	58.8263094	58.8075305	0.0187789
usage_prot_P0CD98	usage_prot_P0CD98	-58.8263094	0.0000000	-58.8075305	0.0000000	58.8263094	58.8075305	0.0187789
usage_prot_P48813	usage_prot_P48813	-58.8263543	0.0000000	-58.8075754	0.0000000	58.8263543	58.8075754	0.0187789
usage_prot_P53322	usage_prot_P53322	-58.8263094	0.0000000	-58.8075305	0.0000000	58.8263094	58.8075305	0.0187789
usage_prot_Q04174	usage_prot_Q04174	-58.8263094	0.0000000	-58.8075305	0.0000000	58.8263094	58.8075305	0.0187789
usage_prot_P38891	usage_prot_P38891	-58.8268918	-0.0005821	-58.8081129	-0.0005821	58.8263098	58.8075309	0.0187789
usage_prot_P40004	usage_prot_P40004	-58.8263094	0.0000000	-58.8075305	0.0000000	58.8263094	58.8075305	0.0187789
usage_prot_Q02895	usage_prot_Q02895	-58.8263094	0.0000000	-58.8075305	0.0000000	58.8263094	58.8075305	0.0187789
usage_prot_P25613	usage_prot_P25613	-58.8560103	-0.0297009	-58.8372314	-0.0297009	58.8263094	58.8075305	0.0187789
usage_prot_P32875	usage_prot_P32875	-58.8263094	0.0000000	-58.8075305	0.0000000	58.8263094	58.8075305	0.0187789
usage_prot_P38827	usage_prot_P38827	-58.8263094	0.0000000	-58.8075305	0.0000000	58.8263094	58.8075305	0.0187789
usage_prot_P40011	usage_prot_P40011	-58.8263094	0.0000000	-58.8075305	0.0000000	58.8263094	58.8075305	0.0187789
usage_prot_Q06494	usage_prot_Q06494	-58.8263094	0.0000000	-58.8075305	0.0000000	58.8263094	58.8075305	0.0187789
usage_prot_Q12256	usage_prot_Q12256	-58.8263094	0.0000000	-58.8075305	0.0000000	58.8263094	58.8075305	0.0187789
usage_prot_Q99271	usage_prot_Q99271	-58.8274896	0.0000000	-58.8087107	0.0000000	58.8274896	58.8087107	0.0187789
usage_prot_Q06005	usage_prot_Q06005	-58.8263094	0.0000000	-58.8075305	0.0000000	58.8263094	58.8075305	0.0187789
usage_prot_P53390	usage_prot_P53390	-59.7360970	0.0000000	-59.7173181	0.0000000	59.7360970	59.7173181	0.0187789
usage_prot_P38628	usage_prot_P38628	-58.8263094	0.0000000	-58.8075305	0.0000000	58.8263094	58.8075305	0.0187789
usage_prot_P15496	usage_prot_P15496	-58.8263133	-0.0000039	-58.8075344	-0.0000039	58.8263094	58.8075305	0.0187789
usage_prot_P07264	usage_prot_P07264	-59.1239069	-0.2975975	-59.1051280	-0.2975975	58.8263094	58.8075305	0.0187789
usage_prot_Q07648	usage_prot_Q07648	-58.8263094	0.0000000	-58.8075305	0.0000000	58.8263094	58.8075305	0.0187789
usage_prot_Q12473	usage_prot_Q12473	-58.8263094	0.0000000	-58.8075305	0.0000000	58.8263094	58.8075305	0.0187789
usage_prot_P40345	usage_prot_P40345	-58.8276529	0.0000000	-58.8088740	0.0000000	58.8276529	58.8088740	0.0187789
usage_prot_P23797	usage_prot_P23797	-58.8263094	0.0000000	-58.8075305	0.0000000	58.8263094	58.8075305	0.0187789
usage_prot_P40039	usage_prot_P40039	-58.8263094	0.0000000	-58.8075305	0.0000000	58.8263094	58.8075305	0.0187789
usage_prot_P38090	usage_prot_P38090	-58.8263094	0.0000000	-58.8075305	0.0000000	58.8263094	58.8075305	0.0187789
usage_prot_P35196	usage_prot_P35196	-58.8263094	0.0000000	-58.8075305	0.0000000	58.8263094	58.8075305	0.0187789
usage_prot_Q04432	usage_prot_Q04432	-58.8263094	0.0000000	-58.8075305	0.0000000	58.8263094	58.8075305	0.0187789
usage_prot_P25297	usage_prot_P25297	-59.1824060	0.0000000	-59.1636271	0.0000000	59.1824060	59.1636271	0.0187789
usage_prot_P38142	usage_prot_P38142	-58.8263094	0.0000000	-58.8075305	0.0000000	58.8263094	58.8075305	0.0187789
usage_prot_Q06685	usage_prot_Q06685	-58.8263094	0.0000000	-58.8075305	0.0000000	58.8263094	58.8075305	0.0187789
usage_prot_P32332	usage_prot_P32332	-59.2085215	0.0000000	-59.1897426	0.0000000	59.2085215	59.1897426	0.0187789
usage_prot_P38127	usage_prot_P38127	-58.8263094	0.0000000	-58.8075305	0.0000000	58.8263094	58.8075305	0.0187789
usage_prot_P38295	usage_prot_P38295	-58.8263094	0.0000000	-58.8075305	0.0000000	58.8263094	58.8075305	0.0187789
usage_prot_P07286	usage_prot_P07286	-58.8263094	0.0000000	-58.8075305	0.0000000	58.8263094	58.8075305	0.0187789
usage_prot_P17505	usage_prot_P17505	-58.8386145	0.0000000	-58.8198355	0.0000000	58.8386145	58.8198355	0.0187789
usage_prot_P53048	usage_prot_P53048	-58.8263094	0.0000000	-58.8075305	0.0000000	58.8263094	58.8075305	0.0187789
usage_prot_P19807	usage_prot_P19807	-58.8263094	0.0000000	-58.8075305	0.0000000	58.8263094	58.8075305	0.0187789
usage_prot_P40582	usage_prot_P40582	-58.8263094	0.0000000	-58.8075305	0.0000000	58.8263094	58.8075305	0.0187789
usage_prot_Q12675	usage_prot_Q12675	-58.8263094	0.0000000	-58.8075305	0.0000000	58.8263094	58.8075305	0.0187789
usage_prot_P33401	usage_prot_P33401	-58.8453040	0.0000000	-58.8265251	0.0000000	58.8453040	58.8265251	0.0187789
usage_prot_P22768	usage_prot_P22768	-58.8500206	-0.0237111	-58.8312417	-0.0237111	58.8263094	58.8075305	0.0187789
usage_prot_P40550	usage_prot_P40550	-58.8263094	0.0000000	-58.8075305	0.0000000	58.8263094	58.8075305	0.0187789
usage_prot_P19145	usage_prot_P19145	-58.8809617	-0.0543512	-58.8621827	-0.0543512	58.8266105	58.8078315	0.0187789
usage_prot_P37012	usage_prot_P37012	-58.8453040	0.0000000	-58.8265251	0.0000000	58.8453040	58.8265251	0.0187789
usage_prot_P38225	usage_prot_P38225	-58.8263094	0.0000000	-58.8075305	0.0000000	58.8263094	58.8075305	0.0187789
usage_prot_Q12390	usage_prot_Q12390	-58.8263094	0.0000000	-58.8075305	0.0000000	58.8263094	58.8075305	0.0187789
usage_prot_P37292	usage_prot_P37292	-58.8263889	0.0000000	-58.8076100	0.0000000	58.8263889	58.8076100	0.0187789
usage_prot_P42884	usage_prot_P42884	-58.8263094	0.0000000	-58.8075305	0.0000000	58.8263094	58.8075305	0.0187789
usage_prot_Q01926	usage_prot_Q01926	-58.8263094	0.0000000	-58.8075305	0.0000000	58.8263094	58.8075305	0.0187789
usage_prot_Q02783	usage_prot_Q02783	-58.8263094	0.0000000	-58.8075305	0.0000000	58.8263094	58.8075305	0.0187789
usage_prot_Q99288	usage_prot_Q99288	-58.8263094	0.0000000	-58.8075305	0.0000000	58.8263094	58.8075305	0.0187789
usage_prot_P38744	usage_prot_P38744	-58.8263094	0.0000000	-58.8075305	0.0000000	58.8263094	58.8075305	0.0187789
usage_prot_P36088	usage_prot_P36088	-58.8263094	0.0000000	-58.8075305	0.0000000	58.8263094	58.8075305	0.0187789
usage_prot_P46995	usage_prot_P46995	-58.8263094	0.0000000	-58.8075305	0.0000000	58.8263094	58.8075305	0.0187789
usage_prot_P32901	usage_prot_P32901	-58.8263094	0.0000000	-58.8075305	0.0000000	58.8263094	58.8075305	0.0187789
usage_prot_P54114	usage_prot_P54114	-58.8263168	0.0000000	-58.8075379	0.0000000	58.8263168	58.8075379	0.0187789
usage_prot_Q04902	usage_prot_Q04902	-58.8263094	0.0000000	-58.8075305	0.0000000	58.8263094	58.8075305	0.0187789
usage_prot_P38221	usage_prot_P38221	-58.8430158	-0.0166438	-58.8242369	-0.0166438	58.8263720	58.8075931	0.0187789
usage_prot_P39979	usage_prot_P39979	-58.8263094	0.0000000	-58.8075305	0.0000000	58.8263094	58.8075305	0.0187789
usage_prot_P39986	usage_prot_P39986	-58.8263094	0.0000000	-58.8075305	0.0000000	58.8263094	58.8075305	0.0187789
usage_prot_Q08295	usage_prot_Q08295	-58.8263094	0.0000000	-58.8075305	0.0000000	58.8263094	58.8075305	0.0187789
usage_prot_P15365	usage_prot_P15365	-58.8263094	0.0000000	-58.8075305	0.0000000	58.8263094	58.8075305	0.0187789
usage_prot_P36010	usage_prot_P36010	-58.8340506	-0.0077154	-58.8152717	-0.0077154	58.8263352	58.8075563	0.0187789
usage_prot_Q12385	usage_prot_Q12385	-58.8263094	0.0000000	-58.8075305	0.0000000	58.8263094	58.8075305	0.0187789
usage_prot_P36007	usage_prot_P36007	-58.8263094	0.0000000	-58.8075305	0.0000000	58.8263094	58.8075305	0.0187789
usage_prot_P38138	usage_prot_P38138	-58.8263094	0.0000000	-58.8075305	0.0000000	58.8263094	58.8075305	0.0187789
usage_prot_P38279	usage_prot_P38279	-58.8263094	0.0000000	-58.8075305	0.0000000	58.8263094	58.8075305	0.0187789
usage_prot_P15019	usage_prot_P15019	-58.8263094	0.0000000	-58.8075305	0.0000000	58.8263094	58.8075305	0.0187789
usage_prot_P32614	usage_prot_P32614	-58.8263094	0.0000000	-58.8075305	0.0000000	58.8263094	58.8075305	0.0187789
usage_prot_P29029	usage_prot_P29029	-58.8263094	0.0000000	-58.8075305	0.0000000	58.8263094	58.8075305	0.0187789
usage_prot_P32375	usage_prot_P32375	-58.8263094	0.0000000	-58.8075305	0.0000000	58.8263094	58.8075305	0.0187789
usage_prot_Q12205	usage_prot_Q12205	-58.8263094	0.0000000	-58.8075305	0.0000000	58.8263094	58.8075305	0.0187789
usage_prot_P25371	usage_prot_P25371	-58.8263094	0.0000000	-58.8075305	0.0000000	58.8263094	58.8075305	0.0187789
usage_prot_P40527	usage_prot_P40527	-58.8263094	0.0000000	-58.8075305	0.0000000	58.8263094	58.8075305	0.0187789
usage_prot_P53730	usage_prot_P53730	-58.8263094	0.0000000	-58.8075305	0.0000000	58.8263094	58.8075305	0.0187789
usage_prot_Q07540	usage_prot_Q07540	-58.8263094	0.0000000	-58.8075305	0.0000000	58.8263094	58.8075305	0.0187789
usage_prot_P50277	usage_prot_P50277	-58.8263094	0.0000000	-58.8075305	0.0000000	58.8263094	58.8075305	0.0187789
usage_prot_P53744	usage_prot_P53744	-58.8263094	0.0000000	-58.8075305	0.0000000	58.8263094	58.8075305	0.0187789
usage_prot_P25360	usage_prot_P25360	-59.1824060	0.0000000	-59.1636271	0.0000000	59.1824060	59.1636271	0.0187789
usage_prot_P47177	usage_prot_P47177	-58.8263094	0.0000000	-58.8075305	0.0000000	58.8263094	58.8075305	0.0187789
usage_prot_P53954	usage_prot_P53954	-58.8263094	0.0000000	-58.8075305	0.0000000	58.8263094	58.8075305	0.0187789
usage_prot_P32906	usage_prot_P32906	-58.8263094	0.0000000	-58.8075305	0.0000000	58.8263094	58.8075305	0.0187789
usage_prot_P15454	usage_prot_P15454	-58.8263183	-0.0000086	-58.8075394	-0.0000086	58.8263098	58.8075309	0.0187789
usage_prot_P25621	usage_prot_P25621	-58.8263094	0.0000000	-58.8075305	0.0000000	58.8263094	58.8075305	0.0187789
usage_prot_P08431	usage_prot_P08431	-58.8687127	0.0000000	-58.8499338	0.0000000	58.8687127	58.8499338	0.0187789
usage_prot_P53208	usage_prot_P53208	-58.8263094	0.0000000	-58.8075305	0.0000000	58.8263094	58.8075305	0.0187789
usage_prot_P25568	usage_prot_P25568	-58.8263094	0.0000000	-58.8075305	0.0000000	58.8263094	58.8075305	0.0187789
usage_prot_P43616	usage_prot_P43616	-58.8263094	0.0000000	-58.8075305	0.0000000	58.8263094	58.8075305	0.0187789
usage_prot_P40360	usage_prot_P40360	-58.8263094	0.0000000	-58.8075305	0.0000000	58.8263094	58.8075305	0.0187789
usage_prot_Q08686	usage_prot_Q08686	-58.8265420	0.0000000	-58.8077631	0.0000000	58.8265420	58.8077631	0.0187789
usage_prot_P53943	usage_prot_P53943	-58.8400631	0.0000000	-58.8212842	0.0000000	58.8400631	58.8212842	0.0187789
usage_prot_Q08992	usage_prot_Q08992	-58.8263094	0.0000000	-58.8075305	0.0000000	58.8263094	58.8075305	0.0187789
usage_prot_Q12055	usage_prot_Q12055	-58.9585640	0.0000000	-58.9397851	0.0000000	58.9585640	58.9397851	0.0187789
usage_prot_P53934	usage_prot_P53934	-58.8263094	0.0000000	-58.8075305	0.0000000	58.8263094	58.8075305	0.0187789
usage_prot_P31755	usage_prot_P31755	-58.8263094	0.0000000	-58.8075305	0.0000000	58.8263094	58.8075305	0.0187789
usage_prot_P38218	usage_prot_P38218	-58.8263094	0.0000000	-58.8075305	0.0000000	58.8263094	58.8075305	0.0187789
usage_prot_Q05911	usage_prot_Q05911	-58.9822061	-0.1558967	-58.9634272	-0.1558967	58.8263094	58.8075305	0.0187789
usage_prot_P41939	usage_prot_P41939	-58.8392039	0.0000000	-58.8204250	0.0000000	58.8392039	58.8204250	0.0187789
usage_prot_P53868	usage_prot_P53868	-58.8263094	0.0000000	-58.8075305	0.0000000	58.8263094	58.8075305	0.0187789
usage_prot_Q06451	usage_prot_Q06451	-58.8263094	0.0000000	-58.8075305	0.0000000	58.8263094	58.8075305	0.0187789
usage_prot_P31115	usage_prot_P31115	-58.8263094	0.0000000	-58.8075305	0.0000000	58.8263094	58.8075305	0.0187789
usage_prot_P53838	usage_prot_P53838	-58.8266649	-0.0003555	-58.8078860	-0.0003555	58.8263094	58.8075305	0.0187789
usage_prot_P19881	usage_prot_P19881	-58.8263094	0.0000000	-58.8075305	0.0000000	58.8263094	58.8075305	0.0187789
usage_prot_P52892	usage_prot_P52892	-58.8282743	0.0000000	-58.8094954	0.0000000	58.8282743	58.8094954	0.0187789
usage_prot_P39109	usage_prot_P39109	-58.8263094	0.0000000	-58.8075305	0.0000000	58.8263094	58.8075305	0.0187789
usage_prot_Q12198	usage_prot_Q12198	-58.8292288	0.0000000	-58.8104499	0.0000000	58.8292288	58.8104499	0.0187789
usage_prot_P19414	usage_prot_P19414	-58.8767687	0.0000000	-58.8579897	0.0000000	58.8767687	58.8579897	0.0187789
usage_prot_P37020	usage_prot_P37020	-58.8263094	0.0000000	-58.8075305	0.0000000	58.8263094	58.8075305	0.0187789
usage_prot_P04397	usage_prot_P04397	-58.8263094	0.0000000	-58.8075305	0.0000000	58.8263094	58.8075305	0.0187789
usage_prot_Q12428	usage_prot_Q12428	-58.8263094	0.0000000	-58.8075305	0.0000000	58.8263094	58.8075305	0.0187789
usage_prot_Q08234	usage_prot_Q08234	-58.8263094	0.0000000	-58.8075305	0.0000000	58.8263094	58.8075305	0.0187789
usage_prot_P40351	usage_prot_P40351	-58.8263094	0.0000000	-58.8075305	0.0000000	58.8263094	58.8075305	0.0187789
usage_prot_P40350	usage_prot_P40350	-58.8263094	0.0000000	-58.8075305	0.0000000	58.8263094	58.8075305	0.0187789
usage_prot_P38921	usage_prot_P38921	-58.8263094	0.0000000	-58.8075305	0.0000000	58.8263094	58.8075305	0.0187789
usage_prot_Q12001	usage_prot_Q12001	-58.8263094	0.0000000	-58.8075305	0.0000000	58.8263094	58.8075305	0.0187789
usage_prot_P50076	usage_prot_P50076	-58.8263094	0.0000000	-58.8075305	0.0000000	58.8263094	58.8075305	0.0187789
usage_prot_P32584	usage_prot_P32584	-58.8263094	0.0000000	-58.8075305	0.0000000	58.8263094	58.8075305	0.0187789
usage_prot_P39007	usage_prot_P39007	-58.8263094	0.0000000	-58.8075305	0.0000000	58.8263094	58.8075305	0.0187789
usage_prot_Q03262	usage_prot_Q03262	-58.8263094	0.0000000	-58.8075305	0.0000000	58.8263094	58.8075305	0.0187789
usage_prot_Q07824	usage_prot_Q07824	-58.8263094	0.0000000	-58.8075305	0.0000000	58.8263094	58.8075305	0.0187789
usage_prot_P12685	usage_prot_P12685	-58.8273885	0.0000000	-58.8086096	0.0000000	58.8273885	58.8086096	0.0187789
usage_prot_Q10740	usage_prot_Q10740	-58.8263094	0.0000000	-58.8075305	0.0000000	58.8263094	58.8075305	0.0187789
usage_prot_P25374	usage_prot_P25374	-58.8263094	0.0000000	-58.8075305	0.0000000	58.8263094	58.8075305	0.0187789
usage_prot_P32318	usage_prot_P32318	-58.8263094	0.0000000	-58.8075305	0.0000000	58.8263094	58.8075305	0.0187789
usage_prot_P53630	usage_prot_P53630	-58.8263094	0.0000000	-58.8075305	0.0000000	58.8263094	58.8075305	0.0187789
usage_prot_Q12116	usage_prot_Q12116	-58.8263094	0.0000000	-58.8075305	0.0000000	58.8263094	58.8075305	0.0187789
usage_prot_standard	usage_prot_standard	-59.4232688	-0.0324781	-59.4044899	-0.0324781	59.3907907	59.3720118	0.0187789
usage_prot_Q08269	usage_prot_Q08269	-58.8277661	-0.0011091	-58.8089872	-0.0011091	58.8266570	58.8078781	0.0187789
usage_prot_P27514	usage_prot_P27514	-59.1824060	0.0000000	-59.1636271	0.0000000	59.1824060	59.1636271	0.0187789
usage_prot_P39713	usage_prot_P39713	-58.8263094	0.0000000	-58.8075305	0.0000000	58.8263094	58.8075305	0.0187789
usage_prot_P32798	usage_prot_P32798	-58.8263094	0.0000000	-58.8075305	0.0000000	58.8263094	58.8075305	0.0187789
usage_prot_P30402	usage_prot_P30402	-58.8378774	0.0000000	-58.8190985	0.0000000	58.8378774	58.8190985	0.0187789
usage_prot_P53394	usage_prot_P53394	-58.8263094	0.0000000	-58.8075305	0.0000000	58.8263094	58.8075305	0.0187789
usage_prot_P47771	usage_prot_P47771	-58.8263168	0.0000000	-58.8075379	0.0000000	58.8263168	58.8075379	0.0187789
usage_prot_P16639	usage_prot_P16639	-58.8263094	0.0000000	-58.8075305	0.0000000	58.8263094	58.8075305	0.0187789
usage_prot_P17898	usage_prot_P17898	-58.7565977	0.0000000	-58.7378501	0.0000000	58.7565977	58.7378501	0.0187477
usage_prot_P47082	usage_prot_P47082	-58.6659296	0.0000000	-58.6472019	0.0000000	58.6659296	58.6472019	0.0187277
usage_prot_P36062	usage_prot_P36062	-58.5711046	0.0000000	-58.5524071	0.0000000	58.5711046	58.5524071	0.0186974
usage_prot_Q06147	usage_prot_Q06147	-58.4181692	0.0000000	-58.3995223	0.0000000	58.4181692	58.3995223	0.0186469
usage_prot_Q12246	usage_prot_Q12246	-58.3714731	0.0000000	-58.3528410	0.0000000	58.3714731	58.3528410	0.0186320
usage_prot_Q12494	usage_prot_Q12494	-58.3048002	0.0000000	-58.2861878	0.0000000	58.3048002	58.2861878	0.0186124
usage_prot_P04710	usage_prot_P04710	-59.1862870	0.0000000	-59.1677598	0.0000000	59.1862870	59.1677598	0.0185272
usage_prot_P18238	usage_prot_P18238	-59.1862870	0.0000000	-59.1677598	0.0000000	59.1862870	59.1677598	0.0185272
usage_prot_P18239	usage_prot_P18239	-59.1862870	0.0000000	-59.1677598	0.0000000	59.1862870	59.1677598	0.0185272
usage_prot_Q12189	usage_prot_Q12189	-58.8791222	-0.0130464	-58.8606031	-0.0130464	58.8660758	58.8475567	0.0185191
usage_prot_P40433	usage_prot_P40433	-57.6876929	0.0000000	-57.6692775	0.0000000	57.6876929	57.6692775	0.0184154
usage_prot_P37254	usage_prot_P37254	-57.6549106	-0.0155936	-57.6365150	-0.0155936	57.6393171	57.6209215	0.0183956
usage_prot_P38358	usage_prot_P38358	-57.2481261	0.0000000	-57.2298510	0.0000000	57.2481261	57.2298510	0.0182751
usage_prot_P28273	usage_prot_P28273	-56.8524343	0.0000000	-56.8342855	0.0000000	56.8524343	56.8342855	0.0181488
usage_prot_Q03778	usage_prot_Q03778	-56.8038781	0.0000000	-56.7857448	0.0000000	56.8038781	56.7857448	0.0181333
usage_prot_P41734	usage_prot_P41734	-56.5807821	0.0000000	-56.5627200	0.0000000	56.5807821	56.5627200	0.0180621
usage_prot_Q12471	usage_prot_Q12471	-56.5264505	0.0000000	-56.5084058	0.0000000	56.5264505	56.5084058	0.0180447
usage_prot_Q12482	usage_prot_Q12482	-58.0903811	0.0000000	-58.0723596	0.0000000	58.0903811	58.0723596	0.0180214
usage_prot_Q07804	usage_prot_Q07804	-56.3325241	0.0000000	-56.3146195	0.0000000	56.3325241	56.3146195	0.0179046
usage_prot_P34163	usage_prot_P34163	-56.1859493	0.0000000	-56.1680912	0.0000000	56.1859493	56.1680912	0.0178581
usage_prot_Q07950	usage_prot_Q07950	-55.6245144	0.0000000	-55.6068348	0.0000000	55.6245144	55.6068348	0.0176796
usage_prot_P23254	usage_prot_P23254	-58.9723840	0.0000000	-58.9547745	0.0000000	58.9723840	58.9547745	0.0176095
usage_prot_P33315	usage_prot_P33315	-58.9723840	0.0000000	-58.9547745	0.0000000	58.9723840	58.9547745	0.0176095
usage_prot_P38075	usage_prot_P38075	-55.0008839	0.0000000	-54.9833262	0.0000000	55.0008839	54.9833262	0.0175577
usage_prot_Q12010	usage_prot_Q12010	-54.9088952	0.0000000	-54.8913668	0.0000000	54.9088952	54.8913668	0.0175284
usage_prot_P54839	usage_prot_P54839	-46.8163586	-1.3851263	-46.7990999	-1.3851263	45.4312324	45.4139737	0.0172587
usage_prot_Q07471	usage_prot_Q07471	-53.1484182	0.0000000	-53.1314518	0.0000000	53.1484182	53.1314518	0.0169664
usage_prot_P37297	usage_prot_P37297	-51.9596353	0.0000000	-51.9430585	0.0000000	51.9596353	51.9430585	0.0165768
usage_prot_P50944	usage_prot_P50944	-51.6112871	0.0000000	-51.5948115	0.0000000	51.6112871	51.5948115	0.0164757
usage_prot_P11986	usage_prot_P11986	-5.5831385	-0.0749881	-5.5666731	-0.0749881	5.5081504	5.4916849	0.0164654
usage_prot_P48016	usage_prot_P48016	-51.2457452	0.0000000	-51.2293862	0.0000000	51.2457452	51.2293862	0.0163590
usage_prot_Q08975	usage_prot_Q08975	-49.8252001	0.0000000	-49.8092946	0.0000000	49.8252001	49.8092946	0.0159055
usage_prot_Q08224	usage_prot_Q08224	-49.8171133	0.0000000	-49.8012104	0.0000000	49.8171133	49.8012104	0.0159029
usage_prot_Q07923	usage_prot_Q07923	-50.1408034	0.0000000	-50.1249591	0.0000000	50.1408034	50.1249591	0.0158443
usage_prot_P32356	usage_prot_P32356	-49.4088632	0.0000000	-49.3930906	0.0000000	49.4088632	49.3930906	0.0157726
usage_prot_Q03941	usage_prot_Q03941	-48.3991074	-0.0050998	-48.3836588	-0.0050998	48.3940076	48.3785590	0.0154486
usage_prot_P35172	usage_prot_P35172	-47.9881195	0.0000000	-47.9728004	0.0000000	47.9881195	47.9728004	0.0153191
usage_prot_Q04301	usage_prot_Q04301	-47.5639583	0.0000000	-47.5487747	0.0000000	47.5639583	47.5487747	0.0151837
usage_prot_P40099	usage_prot_P40099	-47.4981380	0.0000000	-47.4829754	0.0000000	47.4981380	47.4829754	0.0151627
usage_prot_P38331	usage_prot_P38331	-47.0732275	0.0000000	-47.0582005	0.0000000	47.0732275	47.0582005	0.0150270
usage_prot_Q06490	usage_prot_Q06490	-46.5213451	0.0000000	-46.5064942	0.0000000	46.5213451	46.5064942	0.0148508
usage_prot_Q12382	usage_prot_Q12382	-46.3202783	0.0000000	-46.3054917	0.0000000	46.3202783	46.3054917	0.0147867
usage_prot_P41903	usage_prot_P41903	-46.2235138	0.0000000	-46.2087426	0.0000000	46.2235138	46.2087426	0.0147711
usage_prot_P53144	usage_prot_P53144	-46.2405648	0.0000000	-46.2258036	0.0000000	46.2405648	46.2258036	0.0147612
usage_prot_P38994	usage_prot_P38994	-45.8351549	0.0000000	-45.8205320	0.0000000	45.8351549	45.8205320	0.0146229
usage_prot_P54861	usage_prot_P54861	-44.5990534	0.0000000	-44.5848162	0.0000000	44.5990534	44.5848162	0.0142372
usage_prot_Q12283	usage_prot_Q12283	-43.8177965	0.0000000	-43.8038087	0.0000000	43.8177965	43.8038087	0.0139878
usage_prot_P22140	usage_prot_P22140	-43.4269230	0.0000000	-43.4130666	0.0000000	43.4269230	43.4130666	0.0138564
usage_prot_P39104	usage_prot_P39104	-42.4437443	0.0000000	-42.4301952	0.0000000	42.4437443	42.4301952	0.0135492
usage_prot_P23641	usage_prot_P23641	-64.0854917	0.0000000	-64.0721082	0.0000000	64.0854917	64.0721082	0.0133835
usage_prot_P40035	usage_prot_P40035	-64.0854917	0.0000000	-64.0721082	0.0000000	64.0854917	64.0721082	0.0133835
usage_prot_P42951	usage_prot_P42951	-41.8645336	0.0000000	-41.8511775	0.0000000	41.8645336	41.8511775	0.0133561
usage_prot_P00812	usage_prot_P00812	-41.3535322	0.0000000	-41.3403489	0.0000000	41.3535322	41.3403489	0.0131833
usage_prot_Q12525	usage_prot_Q12525	-40.8695948	0.0000000	-40.8565481	0.0000000	40.8695948	40.8565481	0.0130467
usage_prot_Q08985	usage_prot_Q08985	-40.8539508	0.0000000	-40.8409091	0.0000000	40.8539508	40.8409091	0.0130417
usage_prot_Q05979	usage_prot_Q05979	-41.0117074	-0.0803527	-40.9994811	-0.0803527	40.9313547	40.9191284	0.0122263
usage_prot_Q08929	usage_prot_Q08929	-37.3643479	0.0000000	-37.3524202	0.0000000	37.3643479	37.3524202	0.0119277
usage_prot_P22219	usage_prot_P22219	-36.6152812	0.0000000	-36.6035926	0.0000000	36.6152812	36.6035926	0.0116886
usage_prot_P39006	usage_prot_P39006	-37.1496454	0.0000000	-37.1380116	0.0000000	37.1496454	37.1380116	0.0116338
usage_prot_P33330	usage_prot_P33330	-31.5742609	0.0000000	-31.5627294	0.0000000	31.5742609	31.5627294	0.0115315
usage_prot_P32604	usage_prot_P32604	-36.0464330	0.0000000	-36.0349260	0.0000000	36.0464330	36.0349260	0.0115070
usage_prot_P33327	usage_prot_P33327	-28.1966744	0.0000000	-28.1852730	0.0000000	28.1966744	28.1852730	0.0114014
usage_prot_Q04119	usage_prot_Q04119	-45.1767817	0.0000000	-45.1654931	0.0000000	45.1767817	45.1654931	0.0112886
usage_prot_P27515	usage_prot_P27515	-35.2653810	0.0000000	-35.2541234	0.0000000	35.2653810	35.2541234	0.0112576
usage_prot_P39730	usage_prot_P39730	-34.9037243	0.0000000	-34.8925821	0.0000000	34.9037243	34.8925821	0.0111422
usage_prot_P21524	usage_prot_P21524	-34.7636549	0.0000000	-34.7527496	0.0000000	34.7636549	34.7527496	0.0109053
usage_prot_P21672	usage_prot_P21672	-34.4605054	0.0000000	-34.4496951	0.0000000	34.4605054	34.4496951	0.0108102
usage_prot_P53312	usage_prot_P53312	-33.6740109	0.0000000	-33.6632613	0.0000000	33.6740109	33.6632613	0.0107496
usage_prot_P38242	usage_prot_P38242	-32.0019574	0.0000000	-31.9917415	0.0000000	32.0019574	31.9917415	0.0102159
usage_prot_P49090	usage_prot_P49090	-31.2046441	0.0000000	-31.1947496	0.0000000	31.2046441	31.1947496	0.0098945
usage_prot_P49089	usage_prot_P49089	-31.1765035	0.0000000	-31.1666179	0.0000000	31.1765035	31.1666179	0.0098856
usage_prot_P38298	usage_prot_P38298	-30.7082151	0.0000000	-30.6984122	0.0000000	30.7082151	30.6984122	0.0098029
usage_prot_P41909	usage_prot_P41909	-29.8456594	0.0000000	-29.8361319	0.0000000	29.8456594	29.8361319	0.0095275
usage_prot_P25580	usage_prot_P25580	-29.6473118	0.0000000	-29.6378475	0.0000000	29.6473118	29.6378475	0.0094642
usage_prot_P47088	usage_prot_P47088	-29.1789977	0.0000000	-29.1696830	0.0000000	29.1789977	29.1696830	0.0093147
usage_prot_P47052	usage_prot_P47052	-29.0932747	0.0000000	-29.0839889	0.0000000	29.0932747	29.0839889	0.0092858
usage_prot_P53037	usage_prot_P53037	-29.5668909	0.0000000	-29.5576317	0.0000000	29.5668909	29.5576317	0.0092592
usage_prot_P34230	usage_prot_P34230	-28.9806500	0.0000000	-28.9713986	0.0000000	28.9806500	28.9713986	0.0092514
usage_prot_Q00711	usage_prot_Q00711	-28.9402271	0.0000000	-28.9309902	0.0000000	28.9402271	28.9309902	0.0092370
usage_prot_Q12122	usage_prot_Q12122	-26.9944489	0.0000000	-26.9856501	0.0000000	26.9944489	26.9856501	0.0087988
usage_prot_Q8ZND6	usage_prot_Q8ZND6	-30.0669644	0.0000000	-30.0581677	0.0000000	30.0669644	30.0581677	0.0087966
usage_prot_P39932	usage_prot_P39932	-26.8751424	0.0000000	-26.8663751	0.0000000	26.8751424	26.8663751	0.0087673
usage_prot_P40471	usage_prot_P40471	-0.0953348	0.0000000	-0.0953348	-0.0087208	0.0953348	0.0866140	0.0087208
usage_prot_P48570	usage_prot_P48570	-26.5144922	0.0000000	-26.5058498	0.0000000	26.5144922	26.5058498	0.0086424
usage_prot_P53178	usage_prot_P53178	-26.8243520	0.0000000	-26.8157890	0.0000000	26.8243520	26.8157890	0.0085630
usage_prot_P38625	usage_prot_P38625	-26.7339270	-0.3082659	-26.7254912	-0.3082659	26.4256611	26.4172254	0.0084358
usage_prot_P25087	usage_prot_P25087	-29.8860753	0.0000000	-29.8776665	0.0000000	29.8860753	29.8776665	0.0084088
usage_prot_Q07938	usage_prot_Q07938	-30.9941185	-0.0013064	-30.9860501	-0.0013064	30.9928121	30.9847438	0.0080683
usage_prot_P53598	usage_prot_P53598	-25.1522985	0.0000000	-25.1442692	0.0000000	25.1522985	25.1442692	0.0080293
usage_prot_P36136	usage_prot_P36136	-24.9862034	0.0000000	-24.9782271	0.0000000	24.9862034	24.9782271	0.0079763
usage_prot_P47165	usage_prot_P47165	-24.6609538	0.0000000	-24.6530814	0.0000000	24.6609538	24.6530814	0.0078724
usage_prot_P40047	usage_prot_P40047	-23.5115377	0.0000000	-23.5038549	0.0000000	23.5115377	23.5038549	0.0076828
usage_prot_P21595	usage_prot_P21595	-23.7017082	0.0000000	-23.6941420	0.0000000	23.7017082	23.6941420	0.0075662
usage_prot_Q12084	usage_prot_Q12084	-23.2410452	0.0000000	-23.2336260	0.0000000	23.2410452	23.2336260	0.0074192
usage_prot_P09938	usage_prot_P09938	-23.4050973	0.0000000	-23.3977551	0.0000000	23.4050973	23.3977551	0.0073422
usage_prot_P22543	usage_prot_P22543	-22.2107734	0.0000000	-22.2036831	0.0000000	22.2107734	22.2036831	0.0070903
usage_prot_P49723	usage_prot_P49723	-21.4209505	0.0000000	-21.4142308	0.0000000	21.4209505	21.4142308	0.0067197
usage_prot_P40459	usage_prot_P40459	-21.0303187	-0.0019645	-21.0236108	-0.0019645	21.0283543	21.0216463	0.0067079
usage_prot_P53078	usage_prot_P53078	-20.8285904	0.0000000	-20.8219414	0.0000000	20.8285904	20.8219414	0.0066490
usage_prot_P38710	usage_prot_P38710	-20.8266586	0.0000000	-20.8200220	0.0000000	20.8266586	20.8200220	0.0066366
usage_prot_Q05533	usage_prot_Q05533	-20.5247871	0.0000000	-20.5182466	0.0000000	20.5247871	20.5182466	0.0065404
usage_prot_P53154	usage_prot_P53154	-20.2848504	0.0000000	-20.2783749	0.0000000	20.2848504	20.2783749	0.0064755
usage_prot_P53306	usage_prot_P53306	-20.1769030	0.0000000	-20.1704620	0.0000000	20.1769030	20.1704620	0.0064410
usage_prot_P32784	usage_prot_P32784	-22.1771072	0.0000000	-22.1706694	0.0000000	22.1771072	22.1706694	0.0064378
usage_prot_Q12068	usage_prot_Q12068	-20.6201892	0.0000000	-20.6137720	0.0000000	20.6201892	20.6137720	0.0064172
usage_prot_P06776	usage_prot_P06776	-19.4937968	0.0000000	-19.4875739	0.0000000	19.4937968	19.4875739	0.0062229
usage_prot_P36107	usage_prot_P36107	-17.8747498	0.0000000	-17.8690463	0.0000000	17.8747498	17.8690463	0.0057035
usage_prot_P38149	usage_prot_P38149	-17.2602200	0.0000000	-17.2547101	0.0000000	17.2602200	17.2547101	0.0055099
usage_prot_P06197	usage_prot_P06197	-16.8098443	-0.0206546	-16.8044877	-0.0206546	16.7891897	16.7838331	0.0053566
usage_prot_P80210	usage_prot_P80210	-16.3798355	-0.0999791	-16.3745445	-0.0999791	16.2798565	16.2745655	0.0052910
usage_prot_P50942	usage_prot_P50942	-15.4506653	0.0000000	-15.4457331	0.0000000	15.4506653	15.4457331	0.0049323
usage_prot_P40025	usage_prot_P40025	-14.7574754	0.0000000	-14.7527644	0.0000000	14.7574754	14.7527644	0.0047110
usage_prot_P32363	usage_prot_P32363	-14.6957510	0.0000000	-14.6910597	0.0000000	14.6957510	14.6910597	0.0046913
usage_prot_Q12271	usage_prot_Q12271	-14.6895483	0.0000000	-14.6848590	0.0000000	14.6895483	14.6848590	0.0046893
usage_prot_Q02046	usage_prot_Q02046	-11.5595773	0.0000000	-11.5549034	0.0000000	11.5595773	11.5549034	0.0046739
usage_prot_P25578	usage_prot_P25578	-14.5950141	0.0000000	-14.5903568	0.0000000	14.5950141	14.5903568	0.0046574
usage_prot_P25379	usage_prot_P25379	-14.4621668	0.0000000	-14.4575568	0.0000000	14.4621668	14.4575568	0.0046100
usage_prot_Q04178	usage_prot_Q04178	-23.7026953	0.0000000	-23.6980982	0.0000000	23.7026953	23.6980982	0.0045971
usage_prot_Q08911	usage_prot_Q08911	-12.9205629	0.0000000	-12.9160567	0.0000000	12.9205629	12.9160567	0.0045062
usage_prot_P12945	usage_prot_P12945	-14.4001685	0.0000000	-14.3957077	0.0000000	14.4001685	14.3957077	0.0044608
usage_prot_P38143	usage_prot_P38143	-14.6641709	0.0000000	-14.6597205	0.0000000	14.6641709	14.6597205	0.0044503
usage_prot_P25358	usage_prot_P25358	-14.1911990	0.0000000	-14.1868010	0.0000000	14.1911990	14.1868010	0.0043980
usage_prot_Q99190	usage_prot_Q99190	-13.8215100	0.0000000	-13.8172405	0.0000000	13.8215100	13.8172405	0.0042695
usage_prot_P54115	usage_prot_P54115	-13.1638182	0.0000000	-13.1596595	0.0000000	13.1638182	13.1596595	0.0041587
usage_prot_P21801	usage_prot_P21801	-12.6764692	0.0000000	-12.6724232	0.0000000	12.6764692	12.6724232	0.0040460
usage_prot_P00572	usage_prot_P00572	-20.6868884	0.0000000	-20.6828763	0.0000000	20.6868884	20.6828763	0.0040122
usage_prot_P25594	usage_prot_P25594	-12.3444143	0.0000000	-12.3404736	0.0000000	12.3444143	12.3404736	0.0039407
usage_prot_Q12680	usage_prot_Q12680	-12.6759667	0.0000000	-12.6720661	0.0000000	12.6759667	12.6720661	0.0039006
usage_prot_P36126	usage_prot_P36126	-12.0903219	0.0000000	-12.0864624	0.0000000	12.0903219	12.0864624	0.0038595
usage_prot_Q12458	usage_prot_Q12458	-12.0629805	0.0000000	-12.0591297	0.0000000	12.0629805	12.0591297	0.0038508
usage_prot_P06773	usage_prot_P06773	-29.6633951	0.0000000	-29.6595464	0.0000000	29.6633951	29.6595464	0.0038487
usage_prot_P22803	usage_prot_P22803	-12.0886733	0.0000000	-12.0848754	0.0000000	12.0886733	12.0848754	0.0037979
usage_prot_P07149	usage_prot_P07149	-13.0829831	-1.2369181	-13.0792149	-1.2369181	11.8460651	11.8422968	0.0037682
usage_prot_P08678	usage_prot_P08678	-19.0159005	0.0000000	-19.0122125	0.0000000	19.0159005	19.0122125	0.0036881
usage_prot_P25332	usage_prot_P25332	-11.2479878	0.0000000	-11.2443972	0.0000000	11.2479878	11.2443972	0.0035907
usage_prot_P28777	usage_prot_P28777	-12.2173348	-0.2508663	-12.2138736	-0.2508663	11.9664686	11.9630073	0.0034612
usage_prot_Q04396	usage_prot_Q04396	-10.6869639	0.0000000	-10.6835527	0.0000000	10.6869639	10.6835527	0.0034112
usage_prot_P19097	usage_prot_P19097	-11.8390497	-1.1193116	-11.8356397	-1.1193116	10.7197381	10.7163282	0.0034099
usage_prot_P38986	usage_prot_P38986	-10.5962395	0.0000000	-10.5928569	0.0000000	10.5962395	10.5928569	0.0033826
usage_prot_P32327	usage_prot_P32327	-10.8466276	0.0000000	-10.8432515	0.0000000	10.8466276	10.8432515	0.0033761
usage_prot_P11154	usage_prot_P11154	-10.8419795	0.0000000	-10.8386049	0.0000000	10.8419795	10.8386049	0.0033747
usage_prot_P07342	usage_prot_P07342	-9.3598367	-0.1903304	-9.3565348	-0.1903304	9.1695063	9.1662044	0.0033019
usage_prot_Q12325	usage_prot_Q12325	-10.2908650	0.0000000	-10.2876158	0.0000000	10.2908650	10.2876158	0.0032492
usage_prot_Q06346	usage_prot_Q06346	-10.0794398	0.0000000	-10.0762237	0.0000000	10.0794398	10.0762237	0.0032161
usage_prot_P18408	usage_prot_P18408	-10.0449220	-0.0270569	-10.0417479	-0.0270569	10.0178651	10.0146910	0.0031741
usage_prot_P38359	usage_prot_P38359	-9.9728380	0.0000000	-9.9696892	0.0000000	9.9728380	9.9696892	0.0031488
usage_prot_Q02948	usage_prot_Q02948	-9.7550306	0.0000000	-9.7519165	0.0000000	9.7550306	9.7519165	0.0031141
usage_prot_P53045	usage_prot_P53045	-10.9963506	-1.2705156	-10.9932622	-1.2705156	9.7258349	9.7227465	0.0030884
usage_prot_P08566	usage_prot_P08566	-10.6961204	-0.2196302	-10.6930901	-0.2196302	10.4764902	10.4734599	0.0030303
usage_prot_P46961	usage_prot_P46961	-9.3427946	0.0000000	-9.3398121	0.0000000	9.3427946	9.3398121	0.0029825
usage_prot_P18562	usage_prot_P18562	-9.2599724	0.0000000	-9.2570164	0.0000000	9.2599724	9.2570164	0.0029560
usage_prot_P33421	usage_prot_P33421	-9.2535584	0.0000000	-9.2506049	0.0000000	9.2535584	9.2506049	0.0029535
usage_prot_P18544	usage_prot_P18544	-9.8939177	-0.2625235	-9.8909725	-0.2625235	9.6313942	9.6284490	0.0029453
usage_prot_P21147	usage_prot_P21147	-9.8082731	-0.7573691	-9.8053838	-0.7573691	9.0509040	9.0480147	0.0028893
usage_prot_D4YIP5	usage_prot_D4YIP5	-9.7891200	0.0000000	-9.7862560	0.0000000	9.7891200	9.7862560	0.0028640
usage_prot_P14742	usage_prot_P14742	-8.6454834	0.0000000	-8.6427236	0.0000000	8.6454834	8.6427236	0.0027599
usage_prot_P0CX77	usage_prot_P0CX77	-8.5337395	0.0000000	-8.5310153	0.0000000	8.5337395	8.5310153	0.0027242
usage_prot_P0CX78	usage_prot_P0CX78	-8.5337395	0.0000000	-8.5310153	0.0000000	8.5337395	8.5310153	0.0027242
usage_prot_P0CX79	usage_prot_P0CX79	-8.5337395	0.0000000	-8.5310153	0.0000000	8.5337395	8.5310153	0.0027242
usage_prot_P0CZ17	usage_prot_P0CZ17	-8.5337395	0.0000000	-8.5310153	0.0000000	8.5337395	8.5310153	0.0027242
usage_prot_P05694	usage_prot_P05694	-8.9327072	-0.2853156	-8.9299834	-0.2853156	8.6473915	8.6446678	0.0027237
usage_prot_P40559	usage_prot_P40559	-8.4704062	0.0000000	-8.4677022	0.0000000	8.4704062	8.4677022	0.0027040
usage_prot_P37298	usage_prot_P37298	-8.3940795	0.0000000	-8.3914004	0.0000000	8.3940795	8.3914004	0.0026792
usage_prot_P06738	usage_prot_P06738	-13.4022612	0.0000000	-13.3996619	0.0000000	13.4022612	13.3996619	0.0025993
usage_prot_P41835	usage_prot_P41835	-8.1371017	-0.0000008	-8.1345041	-0.0000008	8.1371009	8.1345033	0.0025976
usage_prot_P32567	usage_prot_P32567	-7.9292510	0.0000000	-7.9267222	0.0000000	7.9292510	7.9267222	0.0025287
usage_prot_Q05919	usage_prot_Q05919	-7.8427602	0.0000000	-7.8402566	0.0000000	7.8427602	7.8402566	0.0025036
usage_prot_Q06236	usage_prot_Q06236	-7.8127741	0.0000000	-7.8102805	0.0000000	7.8127741	7.8102805	0.0024936
usage_prot_Q06389	usage_prot_Q06389	-7.7902425	0.0000000	-7.7877557	0.0000000	7.7902425	7.7877557	0.0024869
usage_prot_P53909	usage_prot_P53909	-7.7768529	0.0000000	-7.7743775	0.0000000	7.7768529	7.7743775	0.0024754
usage_prot_P53961	usage_prot_P53961	-7.6908777	0.0000000	-7.6884226	0.0000000	7.6908777	7.6884226	0.0024551
usage_prot_Q01217	usage_prot_Q01217	-8.0951227	-0.2147946	-8.0927129	-0.2147946	7.8803281	7.8779183	0.0024098
usage_prot_P00931	usage_prot_P00931	-8.1817834	-0.1846378	-8.1793967	-0.1846378	7.9971456	7.9947589	0.0023867
usage_prot_P39954	usage_prot_P39954	-7.5171870	-0.1148155	-7.5148243	-0.1148155	7.4023715	7.4000088	0.0023627
usage_prot_P23202	usage_prot_P23202	-7.7765308	0.0000000	-7.7741708	0.0000000	7.7765308	7.7741708	0.0023601
usage_prot_Q12036	usage_prot_Q12036	-7.0854953	0.0000000	-7.0832334	0.0000000	7.0854953	7.0832334	0.0022619
usage_prot_P53871	usage_prot_P53871	-7.0717429	0.0000000	-7.0694854	0.0000000	7.0717429	7.0694854	0.0022575
usage_prot_Q05521	usage_prot_Q05521	-7.0627632	0.0000000	-7.0605086	0.0000000	7.0627632	7.0605086	0.0022546
usage_prot_P28241	usage_prot_P28241	-5.3892009	0.0000000	-5.3870230	0.0000000	5.3892009	5.3870230	0.0021779
usage_prot_P16861	usage_prot_P16861	-5.7013461	0.0000000	-5.6991798	0.0000000	5.7013461	5.6991798	0.0021663
usage_prot_P28834	usage_prot_P28834	-5.3329207	0.0000000	-5.3307656	0.0000000	5.3329207	5.3307656	0.0021551
usage_prot_P43549	usage_prot_P43549	-6.6953915	0.0000000	-6.6932542	0.0000000	6.6953915	6.6932542	0.0021373
usage_prot_P13711	usage_prot_P13711	-7.0350578	0.0000000	-7.0329305	0.0000000	7.0350578	7.0329305	0.0021273
usage_prot_P16862	usage_prot_P16862	-5.5243441	0.0000000	-5.5222450	0.0000000	5.5243441	5.5222450	0.0020991
usage_prot_P39708	usage_prot_P39708	-5.6627337	0.0000000	-5.6607320	0.0000000	5.6627337	5.6607320	0.0020017
usage_prot_P07262	usage_prot_P07262	-5.6567740	0.0000000	-5.6547744	0.0000000	5.6567740	5.6547744	0.0019996
usage_prot_Q04179	usage_prot_Q04179	-6.2443331	0.0000000	-6.2423397	0.0000000	6.2443331	6.2423397	0.0019934
usage_prot_P32264	usage_prot_P32264	-5.3034679	0.0000000	-5.3014945	0.0000000	5.3034679	5.3014945	0.0019734
usage_prot_P47143	usage_prot_P47143	-6.1244073	0.0000000	-6.1224552	0.0000000	6.1244073	6.1224552	0.0019521
usage_prot_Q02196	usage_prot_Q02196	-6.0650372	-0.0163367	-6.0631207	-0.0163367	6.0487005	6.0467840	0.0019165
usage_prot_P38270	usage_prot_P38270	-5.9945957	0.0000000	-5.9926821	0.0000000	5.9945957	5.9926821	0.0019136
usage_prot_P08524	usage_prot_P08524	-6.1574758	-0.2563616	-6.1555920	-0.2563616	5.9011142	5.8992304	0.0018838
usage_prot_P28496	usage_prot_P28496	-5.5548751	0.0000000	-5.5531020	0.0000000	5.5548751	5.5531020	0.0017731
usage_prot_P38703	usage_prot_P38703	-5.4939883	0.0000000	-5.4922346	0.0000000	5.4939883	5.4922346	0.0017537
usage_prot_P40009	usage_prot_P40009	-5.4509189	0.0000000	-5.4491842	0.0000000	5.4509189	5.4491842	0.0017346
usage_prot_P32582	usage_prot_P32582	-4.5715967	0.0000000	-4.5698870	0.0000000	4.5715967	4.5698870	0.0017097
usage_prot_Q08220	usage_prot_Q08220	-5.3145094	0.0000000	-5.3128129	0.0000000	5.3145094	5.3128129	0.0016965
usage_prot_P38972	usage_prot_P38972	-5.6299460	-0.2637358	-5.6282578	-0.2637358	5.3662101	5.3645219	0.0016882
usage_prot_P40445	usage_prot_P40445	-5.3465010	0.0000000	-5.3448134	0.0000000	5.3465010	5.3448134	0.0016875
usage_prot_P06208	usage_prot_P06208	-4.5087532	0.0000000	-4.5070710	0.0000000	4.5087532	4.5070710	0.0016822
usage_prot_P28274	usage_prot_P28274	-5.2209238	0.0000000	-5.2192635	0.0000000	5.2209238	5.2192635	0.0016603
usage_prot_P38627	usage_prot_P38627	-5.2062837	0.0000000	-5.2046280	0.0000000	5.2062837	5.2046280	0.0016557
usage_prot_Q00955	usage_prot_Q00955	-5.7288213	-0.5598855	-5.7271713	-0.5598855	5.1689358	5.1672857	0.0016501
usage_prot_P07244	usage_prot_P07244	-5.2809165	-0.2473855	-5.2793330	-0.2473855	5.0335310	5.0319475	0.0015835
usage_prot_P32288	usage_prot_P32288	-4.9926133	-0.0503763	-4.9910427	-0.0503763	4.9422370	4.9406664	0.0015707
usage_prot_Q06549	usage_prot_Q06549	-4.9035895	0.0000000	-4.9020242	0.0000000	4.9035895	4.9020242	0.0015653
usage_prot_P10963	usage_prot_P10963	-4.7954015	0.0000000	-4.7938707	0.0000000	4.7954015	4.7938707	0.0015308
usage_prot_P21182	usage_prot_P21182	-5.7889554	-0.0002440	-5.7874484	-0.0002440	5.7887114	5.7872044	0.0015070
usage_prot_P25605	usage_prot_P25605	-4.2450694	0.0000000	-4.2435719	0.0000000	4.2450694	4.2435719	0.0014975
usage_prot_Q04894	usage_prot_Q04894	-4.9752968	0.0000000	-4.9738119	0.0000000	4.9752968	4.9738119	0.0014849
usage_prot_P25377	usage_prot_P25377	-4.9442310	0.0000000	-4.9427554	0.0000000	4.9442310	4.9427554	0.0014756
usage_prot_Q04082	usage_prot_Q04082	-4.6144693	0.0000000	-4.6129962	0.0000000	4.6144693	4.6129962	0.0014731
usage_prot_Q06143	usage_prot_Q06143	-4.3173630	0.0000000	-4.3159822	0.0000000	4.3173630	4.3159822	0.0013809
usage_prot_P34756	usage_prot_P34756	-4.2822221	0.0000000	-4.2808551	0.0000000	4.2822221	4.2808551	0.0013670
usage_prot_P17255	usage_prot_P17255	-4.2631952	0.0000000	-4.2618343	0.0000000	4.2631952	4.2618343	0.0013609
usage_prot_P38122	usage_prot_P38122	-4.2278291	-0.0003949	-4.2264806	-0.0003949	4.2274342	4.2260857	0.0013485
usage_prot_P28240	usage_prot_P28240	-3.5430235	0.0000000	-3.5416804	0.0000000	3.5430235	3.5416804	0.0013431
usage_prot_Q06625	usage_prot_Q06625	-6.7810946	0.0000000	-6.7797795	0.0000000	6.7810946	6.7797795	0.0013152
usage_prot_P32179	usage_prot_P32179	-4.1186495	0.0000000	-4.1173480	0.0000000	4.1186495	4.1173480	0.0013015
usage_prot_P22217	usage_prot_P22217	-4.0623432	0.0000000	-4.0610546	0.0000000	4.0623432	4.0610546	0.0012885
usage_prot_P31412	usage_prot_P31412	-4.0336374	0.0000000	-4.0323498	0.0000000	4.0336374	4.0323498	0.0012876
usage_prot_P00937	usage_prot_P00937	-4.2828132	-0.0966500	-4.2815638	-0.0966500	4.1861632	4.1849139	0.0012494
usage_prot_Q03579	usage_prot_Q03579	-3.9019732	0.0000000	-3.9007277	0.0000000	3.9019732	3.9007277	0.0012455
usage_prot_P07347	usage_prot_P07347	-4.0188853	0.0000000	-4.0176404	0.0000000	4.0188853	4.0176404	0.0012449
usage_prot_Q05789	usage_prot_Q05789	-3.8490538	0.0000000	-3.8478251	0.0000000	3.8490538	3.8478251	0.0012287
usage_prot_P04173	usage_prot_P04173	-3.1623996	-0.0692013	-3.1612248	-0.0692013	3.0931983	3.0920235	0.0011748
usage_prot_Q08227	usage_prot_Q08227	-3.6557828	0.0000000	-3.6546165	0.0000000	3.6557828	3.6546165	0.0011663
usage_prot_P10127	usage_prot_P10127	-3.8826611	0.0000000	-3.8815170	0.0000000	3.8826611	3.8815170	0.0011441
usage_prot_P24521	usage_prot_P24521	-3.7242537	-0.1550563	-3.7231144	-0.1550563	3.5691974	3.5680580	0.0011394
usage_prot_P07246	usage_prot_P07246	-3.8144563	0.0000000	-3.8133322	0.0000000	3.8144563	3.8133322	0.0011240
usage_prot_Q08650	usage_prot_Q08650	-3.5407364	0.0000000	-3.5396167	0.0000000	3.5407364	3.5396167	0.0011197
usage_prot_A2P2R3	usage_prot_A2P2R3	-3.4865514	0.0000000	-3.4854384	0.0000000	3.4865514	3.4854384	0.0011130
usage_prot_P38113	usage_prot_P38113	-13.8853103	0.0000000	-13.8842017	0.0000000	13.8853103	13.8842017	0.0011086
usage_prot_P09624	usage_prot_P09624	-4.4208173	0.0000000	-4.4197134	0.0000000	4.4208173	4.4197134	0.0011039
usage_prot_P22434	usage_prot_P22434	-5.6777032	0.0000000	-5.6766021	0.0000000	5.6777032	5.6766021	0.0011012
usage_prot_P32563	usage_prot_P32563	-3.4328142	0.0000000	-3.4317183	0.0000000	3.4328142	3.4317183	0.0010958
usage_prot_P08465	usage_prot_P08465	-3.4592920	-0.0153721	-3.4581998	-0.0153721	3.4439200	3.4428277	0.0010922
usage_prot_P00330	usage_prot_P00330	-13.6088053	0.0000000	-13.6077188	0.0000000	13.6088053	13.6077188	0.0010865
usage_prot_P32473	usage_prot_P32473	-5.2764275	0.0000000	-5.2753593	0.0000000	5.2764275	5.2753593	0.0010681
usage_prot_P00498	usage_prot_P00498	-3.4308856	-0.0429773	-3.4298198	-0.0429773	3.3879083	3.3868425	0.0010658
usage_prot_P21826	usage_prot_P21826	-2.8628457	0.0000000	-2.8617841	0.0000000	2.8628457	2.8617841	0.0010616
usage_prot_P30952	usage_prot_P30952	-2.8627150	0.0000000	-2.8616535	0.0000000	2.8627150	2.8616535	0.0010615
usage_prot_P33317	usage_prot_P33317	-5.3550706	0.0000000	-5.3540321	0.0000000	5.3550706	5.3540321	0.0010385
usage_prot_P39522	usage_prot_P39522	-2.9405815	-0.1028203	-2.9395441	-0.1028203	2.8377612	2.8367238	0.0010374
usage_prot_P38125	usage_prot_P38125	-3.4518630	0.0000000	-3.4508465	0.0000000	3.4518630	3.4508465	0.0010165
usage_prot_P17695	usage_prot_P17695	-3.3358691	0.0000000	-3.3348567	0.0000000	3.3358691	3.3348567	0.0010124
usage_prot_P08432	usage_prot_P08432	-3.1733682	0.0000000	-3.1723574	0.0000000	3.1733682	3.1723574	0.0010108
usage_prot_P07256	usage_prot_P07256	-6.6940838	-0.7200562	-6.6937285	-0.7207035	5.9740277	5.9730250	0.0010027
usage_prot_P06168	usage_prot_P06168	-2.8353763	-0.0991417	-2.8343761	-0.0991417	2.7362346	2.7352343	0.0010002
usage_prot_P37296	usage_prot_P37296	-3.0932556	0.0000000	-3.0922681	0.0000000	3.0932556	3.0922681	0.0009874
usage_prot_P09201	usage_prot_P09201	-3.0602990	0.0000000	-3.0593221	0.0000000	3.0602990	3.0593221	0.0009769
usage_prot_P31116	usage_prot_P31116	-3.0926784	-0.0223924	-3.0917034	-0.0223924	3.0702860	3.0693110	0.0009750
usage_prot_P20967	usage_prot_P20967	-3.5342785	0.0000000	-3.5333680	0.0000000	3.5342785	3.5333680	0.0009105
usage_prot_P50095	usage_prot_P50095	-2.9267921	0.0000000	-2.9258877	0.0000000	2.9267921	2.9258877	0.0009044
usage_prot_P38697	usage_prot_P38697	-2.9240841	0.0000000	-2.9231806	0.0000000	2.9240841	2.9231806	0.0009035
usage_prot_P19657	usage_prot_P19657	-2.9168497	0.0000000	-2.9159468	0.0000000	2.9168497	2.9159468	0.0009029
usage_prot_P07170	usage_prot_P07170	-2.9748595	0.0000000	-2.9739570	0.0000000	2.9748595	2.9739570	0.0009025
usage_prot_P50094	usage_prot_P50094	-2.9173871	0.0000000	-2.9164856	0.0000000	2.9173871	2.9164856	0.0009014
usage_prot_Q08689	usage_prot_Q08689	-2.8721715	0.0000000	-2.8712818	0.0000000	2.8721715	2.8712818	0.0008897
usage_prot_P0CD99	usage_prot_P0CD99	-4.0141170	0.0000000	-4.0132279	0.0000000	4.0141170	4.0132279	0.0008891
usage_prot_P05030	usage_prot_P05030	-2.8473864	0.0000000	-2.8465050	0.0000000	2.8473864	2.8465050	0.0008814
usage_prot_P0CE00	usage_prot_P0CE00	-3.9618560	0.0000000	-3.9609784	0.0000000	3.9618560	3.9609784	0.0008776
usage_prot_P00163	usage_prot_P00163	-5.8182075	-0.6258416	-5.8178986	-0.6264042	5.1923659	5.1914944	0.0008715
usage_prot_P00899	usage_prot_P00899	-2.9473252	-0.0665121	-2.9464654	-0.0665121	2.8808131	2.8799533	0.0008598
usage_prot_P32610	usage_prot_P32610	-2.6648716	0.0000000	-2.6640209	0.0000000	2.6648716	2.6640209	0.0008507
usage_prot_P04806	usage_prot_P04806	-3.1828847	0.0000000	-3.1820456	0.0000000	3.1828847	3.1820456	0.0008390
usage_prot_P17709	usage_prot_P17709	-3.1828847	0.0000000	-3.1820456	0.0000000	3.1828847	3.1820456	0.0008390
usage_prot_P04807	usage_prot_P04807	-3.1828847	0.0000000	-3.1820456	0.0000000	3.1828847	3.1820456	0.0008390
usage_prot_P13181	usage_prot_P13181	-3.7575940	0.0000000	-3.7567617	0.0000000	3.7575940	3.7567617	0.0008323
usage_prot_P52489	usage_prot_P52489	-2.7547966	0.0000000	-2.7539666	0.0000000	2.7547966	2.7539666	0.0008301
usage_prot_P32528	usage_prot_P32528	-2.5922120	0.0000000	-2.5913856	0.0000000	2.5922120	2.5913856	0.0008264
usage_prot_P00549	usage_prot_P00549	-2.7234807	0.0000000	-2.7226600	0.0000000	2.7234807	2.7226600	0.0008206
usage_prot_P07257	usage_prot_P07257	-5.3946629	-0.5802826	-5.3943765	-0.5808043	4.8143803	4.8135722	0.0008080
usage_prot_Q04162	usage_prot_Q04162	-3.6380172	0.0000000	-3.6372114	0.0000000	3.6380172	3.6372114	0.0008058
usage_prot_P25373	usage_prot_P25373	-2.6326654	0.0000000	-2.6318664	0.0000000	2.6326654	2.6318664	0.0007990
usage_prot_P08536	usage_prot_P08536	-2.5162563	0.0000000	-2.5154612	0.0000000	2.5162563	2.5154612	0.0007951
usage_prot_P06106	usage_prot_P06106	-2.4231611	0.0000000	-2.4223961	0.0000000	2.4231611	2.4223961	0.0007650
usage_prot_Q12265	usage_prot_Q12265	-3.9349213	0.0000000	-3.9341659	0.0000000	3.9349213	3.9341659	0.0007554
usage_prot_P62651	usage_prot_P62651	-2.3055139	0.0000000	-2.3047779	0.0000000	2.3055139	2.3047779	0.0007360
usage_prot_P0C5R9	usage_prot_P0C5R9	-2.2786292	0.0000000	-2.2779018	0.0000000	2.2786292	2.2779018	0.0007274
usage_prot_P12684	usage_prot_P12684	-1.9642869	0.0000000	-1.9635627	0.0000000	1.9642869	1.9635627	0.0007241
usage_prot_P12683	usage_prot_P12683	-1.9632006	0.0000000	-1.9624768	0.0000000	1.9632006	1.9624768	0.0007237
usage_prot_P32352	usage_prot_P32352	-2.5432174	0.0000000	-2.5425024	0.0000000	2.5432174	2.5425024	0.0007150
usage_prot_P21954	usage_prot_P21954	-2.0277336	0.0000000	-2.0270236	0.0000000	2.0277336	2.0270236	0.0007100
usage_prot_P29509	usage_prot_P29509	-2.4201386	0.0000000	-2.4194353	0.0000000	2.4201386	2.4194353	0.0007032
usage_prot_Q12166	usage_prot_Q12166	-2.2738771	0.0000000	-2.2731759	0.0000000	2.2738771	2.2731759	0.0007012
usage_prot_P32377	usage_prot_P32377	-2.2595087	-0.0940728	-2.2588174	-0.0940728	2.1654358	2.1647446	0.0006913
usage_prot_P07143	usage_prot_P07143	-4.5386443	-0.4882040	-4.5384034	-0.4886429	4.0504403	4.0497604	0.0006798
usage_prot_P32895	usage_prot_P32895	-3.4852369	0.0000000	-3.4845679	0.0000000	3.4852369	3.4845679	0.0006690
usage_prot_P16140	usage_prot_P16140	-2.0751980	0.0000000	-2.0745355	0.0000000	2.0751980	2.0745355	0.0006625
usage_prot_P23968	usage_prot_P23968	-2.0625964	0.0000000	-2.0619379	0.0000000	2.0625964	2.0619379	0.0006584
usage_prot_P38427	usage_prot_P38427	-2.1272917	0.0000000	-2.1266363	0.0000000	2.1272917	2.1266363	0.0006553
usage_prot_P08679	usage_prot_P08679	-2.0349507	0.0000000	-2.0343161	0.0000000	2.0349507	2.0343161	0.0006346
usage_prot_P38426	usage_prot_P38426	-2.0573984	0.0000000	-2.0567646	0.0000000	2.0573984	2.0567646	0.0006338
usage_prot_P07285	usage_prot_P07285	-2.1480875	-0.0484757	-2.1474609	-0.0484757	2.0996118	2.0989851	0.0006266
usage_prot_P41807	usage_prot_P41807	-1.9554273	0.0000000	-1.9548031	0.0000000	1.9554273	1.9548031	0.0006242
usage_prot_Q12233	usage_prot_Q12233	-10.7601595	0.0000000	-10.7595513	0.0000000	10.7601595	10.7595513	0.0006083
usage_prot_Q12074	usage_prot_Q12074	-1.9086394	0.0000000	-1.9080315	0.0000000	1.9086394	1.9080315	0.0006079
usage_prot_P31688	usage_prot_P31688	-1.7828304	-0.0085384	-1.7822812	-0.0085384	1.7742920	1.7737428	0.0005492
usage_prot_P21623	usage_prot_P21623	-1.8408726	0.0000000	-1.8403305	0.0000000	1.8408726	1.8403305	0.0005421
usage_prot_P28272	usage_prot_P28272	-1.8317311	-0.0207391	-1.8311929	-0.0207391	1.8109920	1.8104538	0.0005382
usage_prot_P17423	usage_prot_P17423	-1.6142914	-0.0098508	-1.6137823	-0.0098508	1.6044406	1.6039315	0.0005091
usage_prot_P38063	usage_prot_P38063	-2.6432806	0.0000000	-2.6427732	0.0000000	2.6432806	2.6427732	0.0005074
usage_prot_P38689	usage_prot_P38689	-2.6009269	0.0000000	-2.6004276	0.0000000	2.6009269	2.6004276	0.0004993
usage_prot_P38620	usage_prot_P38620	-2.5753876	0.0000000	-2.5748932	0.0000000	2.5753876	2.5748932	0.0004944
usage_prot_P16387	usage_prot_P16387	-2.4419581	0.0000000	-2.4414638	0.0000000	2.4419581	2.4414638	0.0004943
usage_prot_Q06408	usage_prot_Q06408	-1.6368284	0.0000000	-1.6363398	0.0000000	1.6368284	1.6363398	0.0004885
usage_prot_P20049	usage_prot_P20049	-1.6837115	-0.0107128	-1.6832292	-0.0107128	1.6729987	1.6725165	0.0004822
usage_prot_P20485	usage_prot_P20485	-1.4987349	0.0000000	-1.4982567	0.0000000	1.4987349	1.4982567	0.0004782
usage_prot_P25515	usage_prot_P25515	-1.4925435	0.0000000	-1.4920671	0.0000000	1.4925435	1.4920671	0.0004765
usage_prot_P08067	usage_prot_P08067	-3.1139458	-0.3349548	-3.1137805	-0.3352560	2.7789909	2.7785245	0.0004664
usage_prot_Q12452	usage_prot_Q12452	-1.6403884	-0.1895301	-1.6399277	-0.1895301	1.4508584	1.4503976	0.0004607
usage_prot_P32366	usage_prot_P32366	-1.4298811	0.0000000	-1.4294246	0.0000000	1.4298811	1.4294246	0.0004565
usage_prot_P10659	usage_prot_P10659	-1.3736786	-0.0206173	-1.3732468	-0.0206174	1.3530613	1.3526295	0.0004319
usage_prot_P07702	usage_prot_P07702	-1.2939599	-0.0578332	-1.2935381	-0.0578332	1.2361266	1.2357049	0.0004218
usage_prot_P53727	usage_prot_P53727	-1.3028744	0.0000000	-1.3024584	0.0000000	1.3028744	1.3024584	0.0004159
usage_prot_P32340	usage_prot_P32340	-1.1360128	0.0000000	-1.1355993	0.0000000	1.1360128	1.1355993	0.0004135
usage_prot_P49435	usage_prot_P49435	-1.5639412	0.0000000	-1.5635341	0.0000000	1.5639412	1.5635341	0.0004071
usage_prot_P19262	usage_prot_P19262	-1.5577996	0.0000000	-1.5573983	0.0000000	1.5577996	1.5573983	0.0004013
usage_prot_P36973	usage_prot_P36973	-1.5194076	0.0000000	-1.5190121	0.0000000	1.5194076	1.5190121	0.0003955
usage_prot_P27796	usage_prot_P27796	-1.2945094	0.0000000	-1.2941180	0.0000000	1.2945094	1.2941180	0.0003914
usage_prot_P40017	usage_prot_P40017	-1.1945896	0.0000000	-1.1942078	0.0000000	1.1945896	1.1942078	0.0003818
usage_prot_P36013	usage_prot_P36013	-1.1425470	0.0000000	-1.1421742	0.0000000	1.1425470	1.1421742	0.0003728
usage_prot_P37303	usage_prot_P37303	-1.1787746	0.0000000	-1.1784022	0.0000000	1.1787746	1.1784022	0.0003724
usage_prot_P00401	usage_prot_P00401	-2.3746187	-0.2868463	-2.3744926	-0.2870867	2.0877724	2.0874059	0.0003665
usage_prot_P00127	usage_prot_P00127	-2.2999085	-0.2473921	-2.2997864	-0.2476145	2.0525164	2.0521719	0.0003445
usage_prot_P53262	usage_prot_P53262	-1.0664726	0.0000000	-1.0661321	0.0000000	1.0664726	1.0661321	0.0003404
usage_prot_P41930	usage_prot_P41930	-1.0510928	0.0000000	-1.0507572	0.0000000	1.0510928	1.0507572	0.0003355
usage_prot_P09368	usage_prot_P09368	-1.1054629	0.0000000	-1.1051325	0.0000000	1.1054629	1.1051325	0.0003305
usage_prot_P38169	usage_prot_P38169	-1.1752137	-0.1423316	-1.1748858	-0.1423316	1.0328821	1.0325541	0.0003280
usage_prot_P28321	usage_prot_P28321	-1.0254010	0.0000000	-1.0250750	0.0000000	1.0254010	1.0250750	0.0003259
usage_prot_P32771	usage_prot_P32771	-1.0916825	0.0000000	-1.0913567	0.0000000	1.0916825	1.0913567	0.0003258
usage_prot_Q08959	usage_prot_Q08959	-1.0154455	0.0000000	-1.0151215	0.0000000	1.0154455	1.0151215	0.0003240
usage_prot_P09457	usage_prot_P09457	-5.6996118	0.0000000	-5.6992896	0.0000000	5.6996118	5.6992896	0.0003222
usage_prot_P53319	usage_prot_P53319	-7.2500979	0.0000000	-7.2497762	0.0000000	7.2500979	7.2497762	0.0003217
usage_prot_P33303	usage_prot_P33303	-2.0903261	0.0000000	-2.0900045	0.0000000	2.0903261	2.0900045	0.0003216
usage_prot_P38720	usage_prot_P38720	-7.2044647	0.0000000	-7.2041450	0.0000000	7.2044647	7.2041450	0.0003197
usage_prot_P22203	usage_prot_P22203	-0.9512297	0.0000000	-0.9509261	0.0000000	0.9512297	0.9509261	0.0003037
usage_prot_Q00764	usage_prot_Q00764	-0.9720941	-0.0046556	-0.9717947	-0.0046556	0.9674385	0.9671390	0.0002995
usage_prot_Q12289	usage_prot_Q12289	-0.9115947	0.0000000	-0.9113034	0.0000000	0.9115947	0.9113034	0.0002913
usage_prot_P00128	usage_prot_P00128	-1.9411350	-0.2088002	-1.9410320	-0.2089879	1.7323348	1.7320441	0.0002908
usage_prot_P80235	usage_prot_P80235	-0.9030428	0.0000000	-0.9027542	0.0000000	0.9030428	0.9027542	0.0002886
usage_prot_P38286	usage_prot_P38286	-0.9132473	0.0000000	-0.9129633	0.0000000	0.9132473	0.9129633	0.0002840
usage_prot_P12695	usage_prot_P12695	-1.3652265	0.0000000	-1.3649502	0.0000000	1.3652265	1.3649502	0.0002764
usage_prot_P21375	usage_prot_P21375	-0.7584507	0.0000000	-0.7581746	0.0000000	0.7584507	0.7581746	0.0002761
usage_prot_P07251	usage_prot_P07251	-4.8806705	0.0000000	-4.8803946	0.0000000	4.8806705	4.8803946	0.0002759
usage_prot_P17649	usage_prot_P17649	-5.9796097	-0.0000002	-5.9793390	-0.0000002	5.9796095	5.9793388	0.0002707
usage_prot_P54885	usage_prot_P54885	-0.7250664	0.0000000	-0.7247966	0.0000000	0.7250664	0.7247966	0.0002698
usage_prot_P39540	usage_prot_P39540	-0.8440955	0.0000000	-0.8438262	0.0000000	0.8440955	0.8438262	0.0002693
usage_prot_P32573	usage_prot_P32573	-0.8611148	0.0000000	-0.8608457	0.0000000	0.8611148	0.8608457	0.0002690
usage_prot_P40495	usage_prot_P40495	-0.8186841	-0.0365909	-0.8184173	-0.0365909	0.7820932	0.7818264	0.0002668
usage_prot_P00830	usage_prot_P00830	-4.5630538	0.0000000	-4.5627959	0.0000000	4.5630538	4.5627959	0.0002580
usage_prot_P47169	usage_prot_P47169	-0.7813779	-0.0021476	-0.7811266	-0.0021476	0.7792302	0.7789789	0.0002513
usage_prot_Q06137	usage_prot_Q06137	-0.7842859	0.0000000	-0.7840355	0.0000000	0.7842859	0.7840355	0.0002504
usage_prot_P38998	usage_prot_P38998	-0.7660914	-0.0342403	-0.7658417	-0.0342403	0.7318512	0.7316015	0.0002497
usage_prot_P16451	usage_prot_P16451	-1.1951331	0.0000000	-1.1948911	0.0000000	1.1951331	1.1948911	0.0002419
usage_prot_Q06178	usage_prot_Q06178	-0.8656309	0.0000000	-0.8653893	0.0000000	0.8656309	0.8653893	0.0002416
usage_prot_P53204	usage_prot_P53204	-0.8479254	0.0000000	-0.8476888	0.0000000	0.8479254	0.8476888	0.0002366
usage_prot_P47125	usage_prot_P47125	-0.8038849	-0.0233182	-0.8036518	-0.0233182	0.7805668	0.7803336	0.0002332
usage_prot_P53311	usage_prot_P53311	-0.6512280	0.0000000	-0.6509963	0.0000000	0.6512280	0.6509963	0.0002318
usage_prot_P53101	usage_prot_P53101	-0.7767773	0.0000000	-0.7765459	0.0000000	0.7767773	0.7765459	0.0002314
usage_prot_P00815	usage_prot_P00815	-0.7371635	-0.0092341	-0.7369345	-0.0092341	0.7279293	0.7277003	0.0002290
usage_prot_P23337	usage_prot_P23337	-1.1689427	0.0000000	-1.1687166	0.0000000	1.1689427	1.1687166	0.0002261
usage_prot_P27472	usage_prot_P27472	-1.1627968	0.0000000	-1.1625719	0.0000000	1.1627968	1.1625719	0.0002249
usage_prot_P08525	usage_prot_P08525	-1.4626816	-0.1573349	-1.4626039	-0.1574763	1.3053467	1.3051276	0.0002191
usage_prot_P32476	usage_prot_P32476	-0.7108286	-0.0295944	-0.7106111	-0.0295944	0.6812342	0.6810167	0.0002175
usage_prot_P54781	usage_prot_P54781	-0.7659551	0.0000000	-0.7657398	0.0000000	0.7659551	0.7657398	0.0002153
usage_prot_P54838	usage_prot_P54838	-0.0717778	0.0000000	-0.0715627	0.0000000	0.0717778	0.0715627	0.0002150
usage_prot_P43550	usage_prot_P43550	-0.0716948	0.0000000	-0.0714800	0.0000000	0.0716948	0.0714800	0.0002148
usage_prot_P53157	usage_prot_P53157	-0.6022829	0.0000000	-0.6020685	0.0000000	0.6022829	0.6020685	0.0002144
usage_prot_P36148	usage_prot_P36148	-0.7208038	-0.0026094	-0.7205956	-0.0026094	0.7181944	0.7179862	0.0002081
usage_prot_P38857	usage_prot_P38857	-0.5846100	0.0000000	-0.5844020	0.0000000	0.5846100	0.5844020	0.0002081
usage_prot_Q06667	usage_prot_Q06667	-0.6470025	0.0000000	-0.6467960	0.0000000	0.6470025	0.6467960	0.0002065
usage_prot_Q99312	usage_prot_Q99312	-0.6462688	0.0000000	-0.6460625	0.0000000	0.6462688	0.6460625	0.0002063
usage_prot_P04161	usage_prot_P04161	-0.6740325	-0.0315752	-0.6738304	-0.0315752	0.6424573	0.6422552	0.0002021
usage_prot_P29704	usage_prot_P29704	-0.6555519	-0.0272930	-0.6553513	-0.0272930	0.6282588	0.6280583	0.0002006
usage_prot_P00817	usage_prot_P00817	-0.6437942	0.0000000	-0.6435963	0.0000000	0.6437942	0.6435963	0.0001979
usage_prot_P32842	usage_prot_P32842	-0.6122210	0.0000000	-0.6120255	0.0000000	0.6122210	0.6120255	0.0001954
usage_prot_P36143	usage_prot_P36143	-1.0067763	0.0000000	-1.0065815	0.0000000	1.0067763	1.0065815	0.0001948
usage_prot_P43635	usage_prot_P43635	-0.9291226	0.0000000	-0.9289297	0.0000000	0.9291226	0.9289297	0.0001929
usage_prot_P53332	usage_prot_P53332	-0.6019444	0.0000000	-0.6017523	0.0000000	0.6019444	0.6017523	0.0001921
usage_prot_P00890	usage_prot_P00890	-0.9214233	0.0000000	-0.9212320	0.0000000	0.9214233	0.9212320	0.0001913
usage_prot_P36165	usage_prot_P36165	-0.6106147	0.0000000	-0.6104248	0.0000000	0.6106147	0.6104248	0.0001900
usage_prot_P00420	usage_prot_P00420	-1.2261203	-0.1481114	-1.2260552	-0.1482355	1.0780089	1.0778197	0.0001892
usage_prot_P38067	usage_prot_P38067	-4.1702597	-0.0000001	-4.1700709	-0.0000001	4.1702596	4.1700708	0.0001888
usage_prot_P39692	usage_prot_P39692	-0.5565401	-0.0015297	-0.5563611	-0.0015297	0.5550104	0.5548315	0.0001790
usage_prot_P00410	usage_prot_P00410	-1.1537081	-0.1393642	-1.1536469	-0.1394810	1.0143439	1.0141659	0.0001781
usage_prot_Q05871	usage_prot_Q05871	-0.5557435	0.0000000	-0.5555698	0.0000000	0.5557435	0.5555698	0.0001736
usage_prot_P37299	usage_prot_P37299	-1.1452230	-0.1231871	-1.1451622	-0.1232979	1.0220359	1.0218644	0.0001715
usage_prot_P07277	usage_prot_P07277	-0.5553327	-0.0231208	-0.5551628	-0.0231208	0.5322119	0.5320420	0.0001699
usage_prot_P22108	usage_prot_P22108	-0.5212996	0.0000000	-0.5211332	0.0000000	0.5212996	0.5211332	0.0001664
usage_prot_P53128	usage_prot_P53128	-0.5419076	0.0000000	-0.5417424	0.0000000	0.5419076	0.5417424	0.0001652
usage_prot_P38077	usage_prot_P38077	-2.8606318	0.0000000	-2.8604701	0.0000000	2.8606318	2.8604701	0.0001617
usage_prot_P38812	usage_prot_P38812	-0.5020217	0.0000000	-0.5018615	0.0000000	0.5020217	0.5018615	0.0001602
usage_prot_P43567	usage_prot_P43567	-0.4215455	0.0000000	-0.4213873	0.0000000	0.4215455	0.4213873	0.0001582
usage_prot_P40319	usage_prot_P40319	-0.5028665	0.0000000	-0.5027094	0.0000000	0.5028665	0.5027094	0.0001571
usage_prot_Q12043	usage_prot_Q12043	-0.5045028	0.0000000	-0.5043459	0.0000000	0.5045028	0.5043459	0.0001570
usage_prot_P00175	usage_prot_P00175	-0.5007024	0.0000000	-0.5005466	0.0000000	0.5007024	0.5005466	0.0001558
usage_prot_P13587	usage_prot_P13587	-0.5021112	0.0000000	-0.5019558	0.0000000	0.5021112	0.5019558	0.0001554
usage_prot_Q01896	usage_prot_Q01896	-0.5019457	0.0000000	-0.5017903	0.0000000	0.5019457	0.5017903	0.0001554
usage_prot_Q12691	usage_prot_Q12691	-0.5018588	0.0000000	-0.5017035	0.0000000	0.5018588	0.5017035	0.0001553
usage_prot_P39111	usage_prot_P39111	-0.4837182	0.0000000	-0.4835637	0.0000000	0.4837182	0.4835637	0.0001544
usage_prot_P81449	usage_prot_P81449	-2.7171464	0.0000000	-2.7169928	0.0000000	2.7171464	2.7169928	0.0001536
usage_prot_P22289	usage_prot_P22289	-0.9963560	-0.1071741	-0.9963031	-0.1072704	0.8891820	0.8890327	0.0001492
usage_prot_P53950	usage_prot_P53950	-0.4643549	0.0000000	-0.4642066	0.0000000	0.4643549	0.4642066	0.0001482
usage_prot_P25340	usage_prot_P25340	-0.5311784	-0.0643267	-0.5310302	-0.0643267	0.4668518	0.4667035	0.0001482
usage_prot_P10869	usage_prot_P10869	-0.4643019	-0.0033618	-0.4641555	-0.0033618	0.4609401	0.4607937	0.0001464
usage_prot_P48836	usage_prot_P48836	-0.4568389	0.0000000	-0.4566931	0.0000000	0.4568389	0.4566931	0.0001458
usage_prot_P16550	usage_prot_P16550	-0.4399114	0.0000000	-0.4397724	0.0000000	0.4399114	0.4397724	0.0001390
usage_prot_P40308	usage_prot_P40308	-0.4308011	0.0000000	-0.4306641	0.0000000	0.4308011	0.4306641	0.0001370
usage_prot_P00854	usage_prot_P00854	-2.4232635	0.0000000	-2.4231266	0.0000000	2.4232635	2.4231266	0.0001370
usage_prot_P08019	usage_prot_P08019	-0.6739840	0.0000000	-0.6738533	0.0000000	0.6739840	0.6738533	0.0001307
usage_prot_P05626	usage_prot_P05626	-2.2422204	0.0000000	-2.2420936	0.0000000	2.2422204	2.2420936	0.0001268
usage_prot_Q99321	usage_prot_Q99321	-0.3945267	0.0000000	-0.3944008	0.0000000	0.3945267	0.3944008	0.0001259
usage_prot_P47011	usage_prot_P47011	-0.6468356	0.0000000	-0.6467105	0.0000000	0.6468356	0.6467105	0.0001251
usage_prot_P00950	usage_prot_P00950	-57.8063681	0.0000000	-57.8062441	0.0000000	57.8063681	57.8062441	0.0001239
usage_prot_P38715	usage_prot_P38715	-0.3965861	0.0000000	-0.3964626	0.0000000	0.3965861	0.3964626	0.0001234
usage_prot_P13663	usage_prot_P13663	-0.3778851	-0.0027361	-0.3777660	-0.0027361	0.3751491	0.3750299	0.0001191
usage_prot_P15274	usage_prot_P15274	-0.3643722	0.0000000	-0.3642538	0.0000000	0.3643722	0.3642538	0.0001184
usage_prot_P42837	usage_prot_P42837	-0.3687081	0.0000000	-0.3685904	0.0000000	0.3687081	0.3685904	0.0001177
usage_prot_Q06708	usage_prot_Q06708	-0.3615583	0.0000000	-0.3614429	0.0000000	0.3615583	0.3614429	0.0001154
usage_prot_P40581	usage_prot_P40581	-0.3710959	0.0000000	-0.3709833	0.0000000	0.3710959	0.3709833	0.0001126
usage_prot_P25641	usage_prot_P25641	-0.3424750	0.0000000	-0.3423660	0.0000000	0.3424750	0.3423660	0.0001090
usage_prot_P32796	usage_prot_P32796	-0.3406346	0.0000000	-0.3405258	0.0000000	0.3406346	0.3405258	0.0001089
usage_prot_P00427	usage_prot_P00427	-0.7003748	-0.0846030	-0.7003376	-0.0846739	0.6157718	0.6156637	0.0001081
usage_prot_P04037	usage_prot_P04037	-0.6923380	-0.0836322	-0.6923012	-0.0837023	0.6087058	0.6085989	0.0001069
usage_prot_P21264	usage_prot_P21264	-0.3346843	-0.0156783	-0.3345840	-0.0156783	0.3190061	0.3189057	0.0001004
usage_prot_Q12031	usage_prot_Q12031	-0.3164367	0.0000000	-0.3163388	0.0000000	0.3164367	0.3163388	0.0000979
usage_prot_P00927	usage_prot_P00927	-0.3063599	0.0000000	-0.3062628	0.0000000	0.3063599	0.3062628	0.0000971
usage_prot_P16603	usage_prot_P16603	-0.3148221	-0.0131072	-0.3147257	-0.0131072	0.3017149	0.3016185	0.0000963
usage_prot_Q3E7B6	usage_prot_Q3E7B6	-0.3011694	0.0000000	-0.3010733	0.0000000	0.3011694	0.3010733	0.0000961
usage_prot_P32799	usage_prot_P32799	-0.6066388	-0.0732800	-0.6066066	-0.0733414	0.5333588	0.5332651	0.0000936
usage_prot_P30902	usage_prot_P30902	-1.6497079	0.0000000	-1.6496147	0.0000000	1.6497079	1.6496147	0.0000933
usage_prot_P14843	usage_prot_P14843	-0.3253827	0.0000000	-0.3252905	0.0000000	0.3253827	0.3252905	0.0000922
usage_prot_P47095	usage_prot_P47095	-0.3538350	-0.0000149	-0.3537429	-0.0000149	0.3538201	0.3537280	0.0000921
usage_prot_P07259	usage_prot_P07259	-0.3049178	-0.0042462	-0.3048284	-0.0042462	0.3006715	0.3005822	0.0000894
usage_prot_P32449	usage_prot_P32449	-0.3149699	0.0000000	-0.3148807	0.0000000	0.3149699	0.3148807	0.0000892
usage_prot_Q04792	usage_prot_Q04792	-1.9367648	0.0000000	-1.9366771	0.0000000	1.9367648	1.9366771	0.0000877
usage_prot_P50113	usage_prot_P50113	-0.2555751	-0.0114229	-0.2554918	-0.0114229	0.2441522	0.2440689	0.0000833
usage_prot_P40545	usage_prot_P40545	-0.2651766	-0.0033218	-0.2650942	-0.0033218	0.2618549	0.2617725	0.0000824
usage_prot_Q08558	usage_prot_Q08558	-0.2634951	0.0000000	-0.2634128	0.0000000	0.2634951	0.2634128	0.0000823
usage_prot_P50264	usage_prot_P50264	-0.3155112	-0.0000133	-0.3154290	-0.0000133	0.3154979	0.3154157	0.0000821
usage_prot_P38139	usage_prot_P38139	-0.2540896	0.0000000	-0.2540088	0.0000000	0.2540896	0.2540088	0.0000808
usage_prot_Q12165	usage_prot_Q12165	-1.4173664	0.0000000	-1.4172863	0.0000000	1.4173664	1.4172863	0.0000801
usage_prot_P28239	usage_prot_P28239	-0.7482264	0.0000000	-0.7481470	0.0000000	0.7482264	0.7481470	0.0000794
usage_prot_P32656	usage_prot_P32656	-0.2427748	0.0000000	-0.2426973	0.0000000	0.2427748	0.2426973	0.0000775
usage_prot_P49095	usage_prot_P49095	-0.3033487	0.0000000	-0.3032717	0.0000000	0.3033487	0.3032717	0.0000770
usage_prot_P10614	usage_prot_P10614	-0.2489970	-0.0103667	-0.2489208	-0.0103667	0.2386303	0.2385541	0.0000762
usage_prot_P19955	usage_prot_P19955	-0.2867106	0.0000000	-0.2866367	0.0000000	0.2867106	0.2866367	0.0000739
usage_prot_P43619	usage_prot_P43619	-0.2454515	-0.0297269	-0.2453830	-0.0297269	0.2157246	0.2156561	0.0000685
usage_prot_Q12349	usage_prot_Q12349	-1.1765307	0.0000000	-1.1764642	0.0000000	1.1765307	1.1764642	0.0000665
usage_prot_Q02207	usage_prot_Q02207	-0.2179198	0.0000000	-0.2178539	0.0000000	0.2179198	0.2178539	0.0000659
usage_prot_P04046	usage_prot_P04046	-0.2190733	-0.0102625	-0.2190076	-0.0102625	0.2088108	0.2087451	0.0000657
usage_prot_Q04409	usage_prot_Q04409	-0.2480072	0.0000000	-0.2479418	0.0000000	0.2480072	0.2479418	0.0000654
usage_prot_P23501	usage_prot_P23501	-0.2001443	0.0000000	-0.2000804	0.0000000	0.2001443	0.2000804	0.0000639
usage_prot_P43601	usage_prot_P43601	-0.1996791	0.0000000	-0.1996154	0.0000000	0.1996791	0.1996154	0.0000637
usage_prot_Q01519	usage_prot_Q01519	-0.3952986	-0.0477508	-0.3952776	-0.0477908	0.3475478	0.3474868	0.0000610
usage_prot_Q12455	usage_prot_Q12455	-0.2267755	-0.0000096	-0.2267165	-0.0000096	0.2267660	0.2267069	0.0000590
usage_prot_P40215	usage_prot_P40215	-1.5878443	0.0000000	-1.5877854	0.0000000	1.5878443	1.5877854	0.0000589
usage_prot_Q07500	usage_prot_Q07500	-1.5601865	0.0000000	-1.5601287	0.0000000	1.5601865	1.5601287	0.0000579
usage_prot_P38604	usage_prot_P38604	-0.1889286	-0.0078658	-0.1888708	-0.0078658	0.1810628	0.1810050	0.0000578
usage_prot_P53315	usage_prot_P53315	-1.3015853	0.0000000	-1.3015276	0.0000000	1.3015853	1.3015276	0.0000578
usage_prot_P38858	usage_prot_P38858	-1.2717783	0.0000000	-1.2717218	0.0000000	1.2717783	1.2717218	0.0000564
usage_prot_P04039	usage_prot_P04039	-0.3597185	-0.0434528	-0.3596994	-0.0434893	0.3162657	0.3162101	0.0000555
usage_prot_Q06405	usage_prot_Q06405	-0.9420240	0.0000000	-0.9419708	0.0000000	0.9420240	0.9419708	0.0000533
usage_prot_P38787	usage_prot_P38787	-0.1645196	-0.0000154	-0.1644671	-0.0000154	0.1645043	0.1644518	0.0000525
usage_prot_Q03266	usage_prot_Q03266	-0.1603429	-0.0000434	-0.1602917	-0.0000434	0.1602995	0.1602484	0.0000512
usage_prot_P05374	usage_prot_P05374	-0.1587525	0.0000000	-0.1587023	0.0000000	0.1587525	0.1587023	0.0000502
usage_prot_P32891	usage_prot_P32891	-0.1526992	0.0000000	-0.1526517	0.0000000	0.1526992	0.1526517	0.0000475
usage_prot_P06785	usage_prot_P06785	-0.1497171	-0.0001241	-0.1496699	-0.0001241	0.1495929	0.1495458	0.0000471
usage_prot_P07991	usage_prot_P07991	-0.1513958	0.0000000	-0.1513495	0.0000000	0.1513958	0.1513495	0.0000463
usage_prot_P05150	usage_prot_P05150	-0.1485222	-0.0040230	-0.1484761	-0.0040230	0.1444992	0.1444531	0.0000461
usage_prot_P32368	usage_prot_P32368	-0.1410136	0.0000000	-0.1409686	0.0000000	0.1410136	0.1409686	0.0000450
usage_prot_P41921	usage_prot_P41921	-0.1430280	0.0000000	-0.1429845	0.0000000	0.1430280	0.1429845	0.0000434
usage_prot_P07255	usage_prot_P07255	-0.2812080	-0.0339690	-0.2811931	-0.0339975	0.2472390	0.2471956	0.0000434
usage_prot_P10174	usage_prot_P10174	-0.2799561	-0.0338178	-0.2799412	-0.0338461	0.2461383	0.2460951	0.0000432
usage_prot_P46681	usage_prot_P46681	-0.1386409	0.0000000	-0.1385977	0.0000000	0.1386409	0.1385977	0.0000431
usage_prot_P40975	usage_prot_P40975	-0.1385692	0.0000000	-0.1385263	0.0000000	0.1385692	0.1385263	0.0000429
usage_prot_P32462	usage_prot_P32462	-0.1347949	-0.0056120	-0.1347536	-0.0056120	0.1291829	0.1291416	0.0000412
usage_prot_P46151	usage_prot_P46151	-0.1348160	0.0000000	-0.1347749	0.0000000	0.1348160	0.1347749	0.0000411
usage_prot_P32353	usage_prot_P32353	-0.1446267	0.0000000	-0.1445860	0.0000000	0.1446267	0.1445860	0.0000407
usage_prot_P39976	usage_prot_P39976	-0.1292035	0.0000000	-0.1291633	0.0000000	0.1292035	0.1291633	0.0000402
usage_prot_P32903	usage_prot_P32903	-0.1286510	0.0000000	-0.1286112	0.0000000	0.1286510	0.1286112	0.0000398
usage_prot_Q01802	usage_prot_Q01802	-0.1247775	0.0000000	-0.1247376	0.0000000	0.1247775	0.1247376	0.0000398
usage_prot_Q05584	usage_prot_Q05584	-0.1249649	0.0000000	-0.1249258	0.0000000	0.1249649	0.1249258	0.0000391
usage_prot_Q12178	usage_prot_Q12178	-0.1161201	0.0000000	-0.1160831	0.0000000	0.1161201	0.1160831	0.0000370
usage_prot_P00425	usage_prot_P00425	-0.6945001	0.0000000	-0.6944632	0.0000000	0.6945001	0.6944632	0.0000369
usage_prot_P00424	usage_prot_P00424	-0.6922168	0.0000000	-0.6921801	0.0000000	0.6922168	0.6921801	0.0000367
usage_prot_P61829	usage_prot_P61829	-0.6461425	0.0000000	-0.6461060	0.0000000	0.6461425	0.6461060	0.0000365
usage_prot_P81451	usage_prot_P81451	-0.6274053	0.0000000	-0.6273699	0.0000000	0.6274053	0.6273699	0.0000355
usage_prot_P05375	usage_prot_P05375	-0.1091578	-0.0025897	-0.1091233	-0.0025897	0.1065681	0.1065336	0.0000345
usage_prot_P00912	usage_prot_P00912	-0.1093366	-0.0024674	-0.1093047	-0.0024674	0.1068692	0.1068373	0.0000319
usage_prot_P21306	usage_prot_P21306	-0.5615336	0.0000000	-0.5615019	0.0000000	0.5615336	0.5615019	0.0000317
usage_prot_P32621	usage_prot_P32621	-0.0991819	0.0000000	-0.0991502	0.0000000	0.0991819	0.0991502	0.0000317
usage_prot_P81450	usage_prot_P81450	-0.5569534	0.0000000	-0.5569219	0.0000000	0.5569534	0.5569219	0.0000315
usage_prot_P47013	usage_prot_P47013	-0.0961887	0.0000000	-0.0961580	0.0000000	0.0961887	0.0961580	0.0000307
usage_prot_P48015	usage_prot_P48015	-0.1178637	0.0000000	-0.1178337	0.0000000	0.1178637	0.1178337	0.0000299
usage_prot_P00045	usage_prot_P00045	-0.0957373	0.0000000	-0.0957075	0.0000000	0.0957373	0.0957075	0.0000298
usage_prot_P53199	usage_prot_P53199	-0.1051691	-0.0121512	-0.1051395	-0.0121512	0.0930179	0.0929883	0.0000295
usage_prot_P00044	usage_prot_P00044	-0.0930676	0.0000000	-0.0930386	0.0000000	0.0930676	0.0930386	0.0000290
usage_prot_P27616	usage_prot_P27616	-0.0959834	-0.0044963	-0.0959546	-0.0044963	0.0914871	0.0914583	0.0000288
usage_prot_P42941	usage_prot_P42941	-0.0770445	0.0000000	-0.0770164	0.0000000	0.0770445	0.0770164	0.0000281
usage_prot_P00856	usage_prot_P00856	-0.4848359	0.0000000	-0.4848085	0.0000000	0.4848359	0.4848085	0.0000274
usage_prot_P13259	usage_prot_P13259	-0.0855019	0.0000000	-0.0854746	0.0000000	0.0855019	0.0854746	0.0000273
usage_prot_Q12375	usage_prot_Q12375	-0.0905246	-0.0024020	-0.0904977	-0.0024020	0.0881227	0.0880957	0.0000269
usage_prot_P07807	usage_prot_P07807	-0.0816882	-0.0000689	-0.0816625	-0.0000689	0.0816193	0.0815936	0.0000257
usage_prot_P50107	usage_prot_P50107	-0.0798415	0.0000000	-0.0798165	0.0000000	0.0798415	0.0798165	0.0000250
usage_prot_Q03835	usage_prot_Q03835	-0.0755887	0.0000000	-0.0755658	0.0000000	0.0755887	0.0755658	0.0000229
usage_prot_P32178	usage_prot_P32178	-0.0790784	-0.0010544	-0.0790558	-0.0010544	0.0780240	0.0780014	0.0000226
usage_prot_P32642	usage_prot_P32642	-0.0735368	0.0000000	-0.0735145	0.0000000	0.0735368	0.0735145	0.0000223
usage_prot_Q08548	usage_prot_Q08548	-0.0767452	0.0000000	-0.0767231	0.0000000	0.0767452	0.0767231	0.0000222
usage_prot_P36014	usage_prot_P36014	-0.0700510	0.0000000	-0.0700298	0.0000000	0.0700510	0.0700298	0.0000213
usage_prot_P32263	usage_prot_P32263	-0.0562212	-0.0003879	-0.0562003	-0.0003879	0.0558333	0.0558124	0.0000209
usage_prot_P11412	usage_prot_P11412	-0.4452131	0.0000000	-0.4451933	0.0000000	0.4452131	0.4451933	0.0000198
usage_prot_P38999	usage_prot_P38999	-0.0518390	-0.0023169	-0.0518221	-0.0023169	0.0495220	0.0495051	0.0000169
usage_prot_P53982	usage_prot_P53982	-0.0467728	0.0000000	-0.0467582	0.0000000	0.0467728	0.0467582	0.0000146
usage_prot_P40015	usage_prot_P40015	-0.0413417	0.0000000	-0.0413285	0.0000000	0.0413417	0.0413285	0.0000132
usage_prot_P39726	usage_prot_P39726	-0.0498102	0.0000000	-0.0497976	0.0000000	0.0498102	0.0497976	0.0000126
usage_prot_Q08108	usage_prot_Q08108	-0.0039153	0.0000000	-0.0039036	0.0000000	0.0039153	0.0039036	0.0000117
usage_prot_P47096	usage_prot_P47096	-0.0368302	-0.0044606	-0.0368200	-0.0044606	0.0323697	0.0323594	0.0000103
usage_prot_Q04066	usage_prot_Q04066	-0.0353908	-0.0010266	-0.0353805	-0.0010266	0.0343642	0.0343540	0.0000103
usage_prot_P33333	usage_prot_P33333	-0.0315874	0.0000000	-0.0315779	0.0000000	0.0315874	0.0315779	0.0000096
usage_prot_P03965	usage_prot_P03965	-0.0490787	-0.0006420	-0.0490701	-0.0006420	0.0484367	0.0484280	0.0000087
usage_prot_P53823	usage_prot_P53823	-2.2651592	0.0000000	-2.2651512	0.0000000	2.2651592	2.2651512	0.0000080
usage_prot_P43544	usage_prot_P43544	-2.2583328	0.0000000	-2.2583249	0.0000000	2.2583328	2.2583249	0.0000080
usage_prot_Q04120	usage_prot_Q04120	-0.0251751	0.0000000	-0.0251674	0.0000000	0.0251751	0.0251674	0.0000076
usage_prot_P16120	usage_prot_P16120	-0.0239667	-0.0001463	-0.0239591	-0.0001463	0.0238204	0.0238129	0.0000076
usage_prot_P03962	usage_prot_P03962	-0.0229505	-0.0002598	-0.0229437	-0.0002598	0.0226906	0.0226839	0.0000067
usage_prot_P32452	usage_prot_P32452	-0.0183000	-0.0001437	-0.0182946	-0.0001437	0.0181563	0.0181509	0.0000054
usage_prot_P52290	usage_prot_P52290	-31.7465092	0.0000000	-31.7465039	0.0000000	31.7465092	31.7465039	0.0000053
usage_prot_Q07729	usage_prot_Q07729	-0.0165271	0.0000000	-0.0165219	0.0000000	0.0165271	0.0165219	0.0000053
usage_prot_Q02979	usage_prot_Q02979	-0.0144436	0.0000000	-0.0144390	0.0000000	0.0144436	0.0144390	0.0000046
usage_prot_P53296	usage_prot_P53296	-24.4937330	0.0000000	-24.4937297	0.0000000	24.4937330	24.4937297	0.0000033
usage_prot_P40353	usage_prot_P40353	-24.1526891	0.0000000	-24.1526858	0.0000000	24.1526891	24.1526858	0.0000033
usage_prot_P07258	usage_prot_P07258	-0.0179664	-0.0002350	-0.0179633	-0.0002350	0.0177314	0.0177282	0.0000032
usage_prot_P32477	usage_prot_P32477	-0.0095058	0.0000000	-0.0095028	0.0000000	0.0095058	0.0095028	0.0000030
usage_prot_P32626	usage_prot_P32626	-0.0107229	-0.0000005	-0.0107201	-0.0000005	0.0107225	0.0107197	0.0000028
usage_prot_Q06497	usage_prot_Q06497	-0.0082955	0.0000000	-0.0082928	0.0000000	0.0082955	0.0082928	0.0000026
usage_prot_Q04958	usage_prot_Q04958	-0.0081177	0.0000000	-0.0081152	0.0000000	0.0081177	0.0081152	0.0000026
usage_prot_Q03677	usage_prot_Q03677	-0.0088889	-0.0000004	-0.0088865	-0.0000004	0.0088885	0.0088862	0.0000023
usage_prot_P06633	usage_prot_P06633	-0.0068423	-0.0000857	-0.0068402	-0.0000857	0.0067566	0.0067545	0.0000021
usage_prot_P38635	usage_prot_P38635	-0.0051760	-0.0000648	-0.0051744	-0.0000648	0.0051112	0.0051096	0.0000016
usage_prot_P08456	usage_prot_P08456	-0.0043456	-0.0002332	-0.0043442	-0.0002332	0.0041124	0.0041110	0.0000014
usage_prot_P07172	usage_prot_P07172	-0.0039495	-0.0000495	-0.0039483	-0.0000495	0.0039000	0.0038988	0.0000012
usage_prot_P38013	usage_prot_P38013	-0.0040116	0.0000000	-0.0040104	0.0000000	0.0040116	0.0040104	0.0000012
usage_prot_P39105	usage_prot_P39105	-0.0031006	0.0000000	-0.0030996	0.0000000	0.0031006	0.0030996	0.0000010
usage_prot_P33734	usage_prot_P33734	-0.0028056	-0.0000351	-0.0028047	-0.0000351	0.0027705	0.0027696	0.0000009
usage_prot_P32190	usage_prot_P32190	-0.0015574	0.0000000	-0.0015569	0.0000000	0.0015574	0.0015569	0.0000005
usage_prot_P53629	usage_prot_P53629	-3.9828948	0.0000000	-3.9828947	0.0000000	3.9828948	3.9828947	0.0000002
usage_prot_P25628	usage_prot_P25628	-30.8222363	0.0000000	-30.8222361	0.0000000	30.8222363	30.8222361	0.0000002
usage_prot_P47147	usage_prot_P47147	-0.0001483	0.0000000	-0.0001482	0.0000000	0.0001483	0.0001482	0.0000000
usage_prot_P06115	usage_prot_P06115	-0.0000990	0.0000000	-0.0000990	0.0000000	0.0000990	0.0000990	0.0000000
usage_prot_P15202	usage_prot_P15202	-0.0000148	0.0000000	-0.0000147	0.0000000	0.0000148	0.0000147	0.0000000
usage_prot_P40506	usage_prot_P40506	-0.0007088	-0.0007088	-0.0007088	-0.0007088	0.0000000	0.0000000	0.0000000
usage_prot_P36076	usage_prot_P36076	-0.0002018	-0.0002018	-0.0002018	-0.0002018	0.0000000	0.0000000	0.0000000
usage_prot_Q04430	usage_prot_Q04430	-0.0001731	-0.0001731	-0.0001731	-0.0001731	0.0000000	0.0000000	0.0000000
usage_prot_P31382	usage_prot_P31382	-0.0411342	0.0000000	-0.0411342	0.0000000	0.0411342	0.0411342	0.0000000
usage_prot_P52867	usage_prot_P52867	-0.0401426	0.0000000	-0.0401426	0.0000000	0.0401426	0.0401426	0.0000000
usage_prot_Q08438	usage_prot_Q08438	-0.0002279	-0.0002279	-0.0002279	-0.0002279	0.0000000	0.0000000	0.0000000
usage_prot_P36024	usage_prot_P36024	-0.0001933	-0.0001933	-0.0001933	-0.0001933	0.0000000	0.0000000	0.0000000
usage_prot_P21373	usage_prot_P21373	-0.0034265	0.0000000	-0.0034265	0.0000000	0.0034265	0.0034265	0.0000000
usage_prot_P32622	usage_prot_P32622	-0.0102713	0.0000000	-0.0102713	0.0000000	0.0102713	0.0102713	0.0000000

Code

# p7 <- pathways |> 
#   column_to_rownames(var = "Description") |> 
#   select(3, 4, 6, 7) |> 
#   #select(where(is.numeric)) |> 
#   pheatmap(color = colorRampPalette(color_de)(50),
#            scale = "row",
#            cluster_rows = TRUE,
#            cluster_cols = TRUE,
#            clustering_distance_rows = "correlation",
#            clustering_distance_cols = "correlation",
#            cutree_rows = 4,
#            cutree_cols = 3,
#            fontsize = 7)
# 
# p7

Code

sessionInfo()

R version 4.2.2 (2022-10-31)
Platform: x86_64-apple-darwin17.0 (64-bit)
Running under: macOS Big Sur ... 10.16

Matrix products: default
BLAS:   /Library/Frameworks/R.framework/Versions/4.2/Resources/lib/libRblas.0.dylib
LAPACK: /Library/Frameworks/R.framework/Versions/4.2/Resources/lib/libRlapack.dylib

locale:
[1] en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8

attached base packages:
[1] stats     graphics  grDevices utils     datasets  methods   base     

other attached packages:
 [1] patchwork_1.1.2     ggVennDiagram_1.2.2 ggrepel_0.9.3      
 [4] Metrics_0.1.4       kableExtra_1.3.4    knitr_1.42         
 [7] lubridate_1.9.2     forcats_1.0.0       stringr_1.5.0      
[10] dplyr_1.1.0         purrr_1.0.1         readr_2.1.4        
[13] tidyr_1.3.0         tibble_3.2.0        ggplot2_3.4.1      
[16] tidyverse_2.0.0    

loaded via a namespace (and not attached):
 [1] httr_1.4.5         bit64_4.0.5        vroom_1.6.1        jsonlite_1.8.4    
 [5] viridisLite_0.4.1  splines_4.2.2      highr_0.10         yaml_2.3.7        
 [9] pillar_1.8.1       lattice_0.20-45    glue_1.6.2         limma_3.54.0      
[13] digest_0.6.31      rvest_1.0.3        RVenn_1.1.0        colorspace_2.1-0  
[17] htmltools_0.5.4    Matrix_1.5-3       pkgconfig_2.0.3    scales_1.2.1      
[21] webshot_0.5.4      svglite_2.1.1      tzdb_0.3.0         timechange_0.2.0  
[25] proxy_0.4-27       mgcv_1.8-42        generics_0.1.3     farver_2.1.1      
[29] ellipsis_0.3.2     withr_2.5.0        cli_3.6.0          magrittr_2.0.3    
[33] crayon_1.5.2       evaluate_0.20      fansi_1.0.4        nlme_3.1-162      
[37] xml2_1.3.3         class_7.3-21       textshaping_0.3.6  tools_4.2.2       
[41] hms_1.1.2          lifecycle_1.0.3    munsell_0.5.0      compiler_4.2.2    
[45] e1071_1.7-13       systemfonts_1.0.4  rlang_1.0.6        classInt_0.4-9    
[49] units_0.8-1        grid_4.2.2         rstudioapi_0.14    htmlwidgets_1.6.1 
[53] labeling_0.4.2     rmarkdown_2.20     gtable_0.3.1       DBI_1.1.3         
[57] R6_2.5.1           fastmap_1.1.1      bit_4.0.5          utf8_1.2.3        
[61] ragg_1.2.5         KernSmooth_2.23-20 stringi_1.7.12     parallel_4.2.2    
[65] Rcpp_1.0.10        vctrs_0.5.2        sf_1.0-12          tidyselect_1.2.0  
[69] xfun_0.37