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 : aacoa_c
List of minimal gene deletion strategies (Download)

Gene deletion strategy (84 of 84: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 75
  Gene deletion: b2836 b3553 b1478 b4382 b3942 b1732 b0474 b2518 b1241 b0351 b4069 b2502 b4384 b2744 b3708 b1479 b3752 b2297 b2458 b2926 b2781 b0099 b3617 b3124 b3236 b2883 b3962 b1982 b0104 b2797 b3117 b1814 b4471 b4267 b1033 b0595 b1623 b1415 b3551 b1014 b4014 b0261 b2976 b2799 b3945 b3709 b1907 b4219 b1832 b1778 b2406 b3161 b0112 b2789 b3127 b2868 b4265 b4064 b4464 b0114 b1539 b2492 b0904 b2954 b1533 b1380 b1710 b2480 b1473 b0494 b0514 b4266 b3662 b1985 b4209   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.221983 (mmol/gDw/h)
  Minimum Production Rate : 0.471984 (mmol/gDw/h)

Substrate: (mmol/gDw/h)
  EX_o2_e : 32.075463
  EX_glc__D_e : 10.000000
  EX_nh4_e : 5.894808
  EX_pi_e : 1.630079
  EX_so4_e : 0.720159
  EX_k_e : 0.043330
  EX_mg2_e : 0.001926
  EX_fe2_e : 0.001832
  EX_fe3_e : 0.001733
  EX_ca2_e : 0.001155
  EX_cl_e : 0.001155
  EX_cu2_e : 0.000157
  EX_mn2_e : 0.000153
  EX_zn2_e : 0.000076
  EX_ni2_e : 0.000072

Product: (mmol/gDw/h)
  EX_h2o_e : 49.661440
  EX_co2_e : 33.501639
  EX_h_e : 5.578227
  EX_ac_e : 2.311753
  Auxiliary production reaction : 0.471984
  EX_met__L_e : 0.192275
  EX_ade_e : 0.000248
  DM_5drib_c : 0.000149
  EX_dxylnt_e : 0.000149
  DM_4crsol_c : 0.000050

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