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 : mal__L_c
List of minimal gene deletion strategies (Download)

Gene deletion strategy (10 of 29: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 32
  Gene deletion: b3553 b1478 b3942 b1732 b1241 b0351 b2779 b1004 b3713 b1109 b0046 b3236 b2463 b2210 b1033 b3551 b1602 b4219 b1832 b1778 b3915 b0529 b1380 b1710 b2480 b1771 b1206 b0606 b0221 b2285 b1009 b4209   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.572570 (mmol/gDw/h)
  Minimum Production Rate : 0.597072 (mmol/gDw/h)

 Substrate: (mmol/gDw/h)
  EX_o2_e : 33.273408
  EX_glc__D_e : 10.000000
  EX_nh4_e : 6.183713
  EX_pi_e : 0.552305
  EX_so4_e : 0.144185
  EX_k_e : 0.111762
  EX_fe3_e : 0.009196
  EX_mg2_e : 0.004967
  EX_ca2_e : 0.002980
  EX_cl_e : 0.002980
  EX_cu2_e : 0.000406
  EX_mn2_e : 0.000396
  EX_zn2_e : 0.000195
  EX_ni2_e : 0.000185
  EX_cobalt2_e : 0.000014

Product: (mmol/gDw/h)
  EX_h2o_e : 49.612990
  EX_co2_e : 33.952966
  EX_h_e : 6.464346
  Auxiliary production reaction : 0.597072
  EX_12ppd__R_e : 0.052453
  DM_5drib_c : 0.000129
  DM_4crsol_c : 0.000128

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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