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 (9 of 14: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 41
  Gene deletion: b1478 b3942 b1732 b1241 b0351 b4069 b1479 b2297 b2458 b2779 b3617 b3236 b2463 b3962 b0104 b2210 b4267 b1415 b3551 b1014 b3945 b4138 b4123 b0621 b2913 b4219 b1832 b1778 b0114 b0509 b3125 b1539 b2835 b1380 b0325 b1710 b2480 b0494 b4266 b1206 b4209   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.556613 (mmol/gDw/h)
  Minimum Production Rate : 0.098312 (mmol/gDw/h)

 Substrate: (mmol/gDw/h)
  EX_o2_e : 33.168724
  EX_glc__D_e : 10.000000
  EX_nh4_e : 6.011372
  EX_pi_e : 0.536912
  EX_so4_e : 0.140166
  EX_k_e : 0.108647
  EX_mg2_e : 0.004829
  EX_fe2_e : 0.004594
  EX_fe3_e : 0.004346
  EX_ca2_e : 0.002897
  EX_cl_e : 0.002897
  EX_cu2_e : 0.000395
  EX_mn2_e : 0.000385
  EX_zn2_e : 0.000190
  EX_ni2_e : 0.000180
  EX_cobalt2_e : 0.000014

Product: (mmol/gDw/h)
  EX_h2o_e : 49.053883
  EX_co2_e : 34.259136
  EX_h_e : 6.565399
  EX_ac_e : 1.249676
  EX_mal__L_e : 0.098312
  EX_dxylnt_e : 0.000372
  DM_5drib_c : 0.000125
  DM_4crsol_c : 0.000124

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
Contact