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 : dudp_c
List of minimal gene deletion strategies (Download)

Gene deletion strategy (74 of 77: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 49
  Gene deletion: b3553 b0238 b0125 b4069 b2744 b3708 b3926 b2297 b2458 b2926 b1004 b3713 b1109 b0046 b3236 b2883 b0477 b2797 b3117 b1814 b4471 b3449 b1033 b4374 b2361 b2291 b0411 b1602 b2913 b3654 b2868 b3714 b3664 b4064 b4464 b0114 b0529 b1539 b2492 b0904 b1533 b3927 b1380 b0494 b1511 b3662 b0606 b2285 b4209   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.449565 (mmol/gDw/h)
  Minimum Production Rate : 0.534120 (mmol/gDw/h)

Substrate: (mmol/gDw/h)
  EX_o2_e : 35.711025
  EX_glc__D_e : 10.000000
  EX_nh4_e : 5.923503
  EX_pi_e : 1.501894
  EX_so4_e : 0.113209
  EX_k_e : 0.087752
  EX_fe3_e : 0.007220
  EX_mg2_e : 0.003900
  EX_cl_e : 0.002340
  EX_ca2_e : 0.002340
  EX_cu2_e : 0.000319
  EX_mn2_e : 0.000311
  EX_zn2_e : 0.000153
  EX_ni2_e : 0.000145
  EX_cobalt2_e : 0.000011

Product: (mmol/gDw/h)
  EX_h2o_e : 52.279207
  EX_co2_e : 36.138090
  EX_h_e : 4.972746
  Auxiliary production reaction : 0.534120
  EX_ac_e : 0.300624
  DM_mththf_c : 0.000201
  DM_5drib_c : 0.000101
  DM_4crsol_c : 0.000100

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