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 : dutp_c
List of minimal gene deletion strategies (Download)

Gene deletion strategy (35 of 79: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 31
  Gene deletion: b4382 b3942 b1732 b1241 b0351 b4069 b4384 b2930 b4232 b3697 b3925 b0871 b2297 b2458 b3617 b0030 b2407 b3236 b1779 b1982 b3946 b2210 b0825 b0411 b2406 b0114 b0529 b2492 b0904 b1517 b2285   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.294080 (mmol/gDw/h)
  Minimum Production Rate : 1.127587 (mmol/gDw/h)

Substrate: (mmol/gDw/h)
  EX_fe2_e : 1000.000000
  EX_h_e : 993.459028
  EX_o2_e : 278.909827
  EX_glc__D_e : 10.000000
  EX_nh4_e : 5.431409
  EX_pi_e : 3.666432
  EX_so4_e : 0.074055
  EX_k_e : 0.057402
  EX_mg2_e : 0.002551
  EX_ca2_e : 0.001531
  EX_cl_e : 0.001531
  EX_cu2_e : 0.000209
  EX_mn2_e : 0.000203
  EX_zn2_e : 0.000100
  EX_ni2_e : 0.000095

Product: (mmol/gDw/h)
  EX_fe3_e : 999.995277
  EX_h2o_e : 548.024728
  EX_co2_e : 26.708818
  EX_pyr_e : 3.403758
  Auxiliary production reaction : 1.127587
  EX_ac_e : 0.429972
  DM_oxam_c : 0.000198
  EX_mththf_e : 0.000132
  DM_5drib_c : 0.000066
  DM_4crsol_c : 0.000066

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