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 : uacmam_c
List of minimal gene deletion strategies (Download)

Gene deletion strategy (63 of 83: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 26
  Gene deletion: b3831 b2744 b3614 b0910 b3752 b4152 b2781 b1612 b1611 b4122 b1759 b4374 b2361 b2291 b0411 b3945 b4388 b4138 b4123 b0621 b0452 b2197 b3825 b3918 b4042 b1206   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.680438 (mmol/gDw/h)
  Minimum Production Rate : 0.097379 (mmol/gDw/h)

Substrate: (mmol/gDw/h)
  EX_fe2_e : 1000.000000
  EX_h_e : 991.450147
  EX_o2_e : 275.660672
  EX_glc__D_e : 10.000000
  EX_nh4_e : 8.411108
  EX_pi_e : 0.851112
  EX_so4_e : 0.171348
  EX_k_e : 0.132817
  EX_mg2_e : 0.005903
  EX_ca2_e : 0.003542
  EX_cl_e : 0.003542
  EX_cu2_e : 0.000482
  EX_mn2_e : 0.000470
  EX_zn2_e : 0.000232
  EX_ni2_e : 0.000220
  EX_cobalt2_e : 0.000017

Product: (mmol/gDw/h)
  EX_fe3_e : 999.989071
  EX_h2o_e : 547.706390
  EX_co2_e : 26.036898
  EX_succ_e : 0.709555
  EX_ura_e : 0.385152
  Auxiliary production reaction : 0.097379
  DM_5drib_c : 0.000153
  DM_4crsol_c : 0.000152

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