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 : cdpdhdecg_c
List of minimal gene deletion strategies (Download)

Gene deletion strategy (54 of 71: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 25
  Gene deletion: b1054 b0474 b2518 b3831 b4152 b2781 b0030 b1612 b1611 b4122 b0651 b2162 b1759 b2440 b4161 b4138 b4123 b0621 b4381 b2406 b2197 b3918 b1912 b0494 b1206   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.562365 (mmol/gDw/h)
  Minimum Production Rate : 0.297010 (mmol/gDw/h)

Substrate: (mmol/gDw/h)
  EX_fe2_e : 1000.000000
  EX_h_e : 993.150288
  EX_o2_e : 266.478602
  EX_glc__D_e : 10.000000
  EX_nh4_e : 7.168101
  EX_pi_e : 1.136481
  EX_so4_e : 0.141615
  EX_k_e : 0.109770
  EX_mg2_e : 0.004879
  EX_ca2_e : 0.002927
  EX_cl_e : 0.002927
  EX_cu2_e : 0.000399
  EX_mn2_e : 0.000389
  EX_zn2_e : 0.000192
  EX_ni2_e : 0.000182
  EX_cobalt2_e : 0.000014

Product: (mmol/gDw/h)
  EX_fe3_e : 999.990968
  EX_h2o_e : 540.304660
  EX_co2_e : 21.096190
  EX_succ_e : 0.586429
  Auxiliary production reaction : 0.297010
  EX_ura_e : 0.101790
  DM_5drib_c : 0.000127
  DM_4crsol_c : 0.000125

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