MetNetComp Database [1] / Minimal gene deletions

Minimal gene deletions for simulation-based growth-coupled production. You can also see maximal gene deletions.


Model : iML1515 [2].
Target metabolite : urdglyc_c
List of minimal gene deletion strategies (Download)

Gene deletion strategy (66 of 74: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 34
  Gene deletion: b3553 b4269 b0493 b3588 b3003 b3011 b3926 b0871 b1004 b3713 b1109 b0046 b3236 b1638 b4139 b1033 b1602 b0507 b2913 b4381 b3654 b3714 b3664 b0511 b4064 b4464 b0114 b0529 b2492 b0904 b3029 b1380 b1518 b2285   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.506985 (mmol/gDw/h)
  Minimum Production Rate : 0.136226 (mmol/gDw/h)

Substrate: (mmol/gDw/h)
  EX_o2_e : 37.971331
  EX_glc__D_e : 10.000000
  EX_nh4_e : 5.747844
  EX_pi_e : 0.489040
  EX_so4_e : 0.127669
  EX_k_e : 0.098960
  EX_fe2_e : 0.008143
  EX_mg2_e : 0.004398
  EX_ca2_e : 0.002639
  EX_cl_e : 0.002639
  EX_cu2_e : 0.000359
  EX_mn2_e : 0.000350
  EX_zn2_e : 0.000173
  EX_ni2_e : 0.000164
  EX_cobalt2_e : 0.000013

Product: (mmol/gDw/h)
  EX_h2o_e : 52.577536
  EX_co2_e : 38.780794
  EX_h_e : 5.067056
  Auxiliary production reaction : 0.136226
  DM_mththf_c : 0.000227
  DM_5drib_c : 0.000114
  DM_4crsol_c : 0.000113

Visualization
  1. Download JSON file.
  2. Go to Escher site [3].
  3. Select "Data > Load reaction data" and apply the downloaded file.

References
[1] Tamura, T. MetNetComp: Database for minimal and maximal gene deletion strategies for growth-coupled production of genome-scale metabolic networks, IEEE/ACM Transactions on Computational Biology and Bioinformatics, in press.
[2] Norsigian, C. J., Pusarla, N., McConn, J. L., Yurkovich, J. T., Dräger, A., Palsson, B. O., & King, Z. (2020). BiGG Models 2020: multi-strain genome-scale models and expansion across the phylogenetic tree. Nucleic acids research, 48(D1), D402-D406.
[3] King, Z. A., Dräger, A., Ebrahim, A., Sonnenschein, N., Lewis, N. E., & Palsson, B. O. (2015). Escher: a web application for building, sharing, and embedding data-rich visualizations of biological pathways. PLoS computational biology, 11(8), e1004321.


Last updated: 21-Sep-2023
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