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 : dcamp_c
List of minimal gene deletion strategies (Download)

Gene deletion strategy (32 of 77: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 25
  Gene deletion: b3399 b4382 b4269 b0493 b3588 b3003 b3011 b1241 b0351 b2502 b4384 b2744 b0871 b1982 b3616 b3589 b0675 b2361 b0261 b4381 b0112 b0114 b0529 b2492 b0904   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.577411 (mmol/gDw/h)
  Minimum Production Rate : 0.456233 (mmol/gDw/h)

Substrate: (mmol/gDw/h)
  EX_o2_e : 21.112556
  EX_nh4_e : 10.446272
  EX_glc__D_e : 10.000000
  EX_pi_e : 1.013207
  EX_so4_e : 0.145404
  EX_k_e : 0.112707
  EX_fe2_e : 0.009274
  EX_mg2_e : 0.005009
  EX_cl_e : 0.003005
  EX_ca2_e : 0.003005
  EX_cu2_e : 0.000409
  EX_mn2_e : 0.000399
  EX_zn2_e : 0.000197
  EX_ni2_e : 0.000187
  EX_cobalt2_e : 0.000014

Product: (mmol/gDw/h)
  EX_h2o_e : 47.688239
  EX_co2_e : 20.265796
  EX_h_e : 10.428232
  EX_thymd_e : 0.964558
  Auxiliary production reaction : 0.456233
  DM_5drib_c : 0.000387
  DM_4crsol_c : 0.000129

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