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_e
List of minimal gene deletion strategies (Download)

Gene deletion strategy (8 of 14: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 40
  Gene deletion: b4467 b1478 b3942 b1732 b1241 b0351 b2925 b2097 b3844 b1004 b3713 b1109 b0046 b2690 b2463 b2210 b3551 b2799 b3945 b1602 b4138 b4123 b0621 b4219 b1832 b1778 b0755 b3612 b0529 b1539 b2492 b0904 b1380 b1710 b2480 b1695 b1206 b0606 b2285 b1008   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.422207 (mmol/gDw/h)
  Minimum Production Rate : 0.479386 (mmol/gDw/h)

 Substrate: (mmol/gDw/h)
  EX_o2_e : 32.519149
  EX_glc__D_e : 10.000000
  EX_nh4_e : 4.559799
  EX_pi_e : 0.407263
  EX_so4_e : 0.106320
  EX_k_e : 0.082412
  EX_fe2_e : 0.006781
  EX_mg2_e : 0.003663
  EX_ca2_e : 0.002198
  EX_cl_e : 0.002198
  EX_cu2_e : 0.000299
  EX_mn2_e : 0.000292
  EX_zn2_e : 0.000144
  EX_ni2_e : 0.000136
  EX_cobalt2_e : 0.000011

Product: (mmol/gDw/h)
  EX_h2o_e : 44.569465
  EX_co2_e : 32.940761
  EX_h_e : 8.744198
  EX_ac_e : 3.906019
  EX_mal__L_e : 0.479386
  DM_5drib_c : 0.000095
  DM_4crsol_c : 0.000094

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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