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 : gsn_c
List of minimal gene deletion strategies (Download)

Gene deletion strategy (78 of 79: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 49
  Gene deletion: b4269 b3942 b1732 b0493 b3588 b3003 b3011 b1241 b0351 b2744 b1479 b0871 b2926 b3844 b3236 b2883 b2463 b3962 b0104 b3616 b3589 b2210 b4267 b1415 b3551 b1014 b0261 b3945 b4219 b1832 b1778 b4381 b0112 b2868 b4064 b4464 b0114 b0755 b3612 b0529 b2492 b0904 b1380 b0325 b1710 b2480 b0508 b0514 b4266   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.373213 (mmol/gDw/h)
  Minimum Production Rate : 0.492833 (mmol/gDw/h)

Substrate: (mmol/gDw/h)
  EX_o2_e : 36.348023
  EX_glc__D_e : 10.000000
  EX_nh4_e : 7.065821
  EX_pi_e : 0.360003
  EX_so4_e : 0.093982
  EX_k_e : 0.072849
  EX_fe2_e : 0.005994
  EX_mg2_e : 0.003238
  EX_ca2_e : 0.001943
  EX_cl_e : 0.001943
  EX_cu2_e : 0.000265
  EX_mn2_e : 0.000258
  EX_zn2_e : 0.000127
  EX_ni2_e : 0.000121

Product: (mmol/gDw/h)
  EX_h2o_e : 52.559091
  EX_co2_e : 36.140431
  EX_h_e : 6.464632
  EX_acald_e : 1.520164
  Auxiliary production reaction : 0.492833
  EX_ade_e : 0.114198
  EX_dxylnt_e : 0.000250
  DM_5drib_c : 0.000084
  DM_4crsol_c : 0.000083

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