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 : dhpmp_c
List of minimal gene deletion strategies (Download)

Gene deletion strategy (104 of 116: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 47
  Gene deletion: b4467 b1478 b3399 b4269 b0493 b3588 b3003 b3011 b1241 b4384 b2744 b0871 b2926 b0160 b1004 b3713 b1109 b0046 b3236 b1638 b4139 b3665 b4374 b0675 b2361 b2291 b4015 b2799 b3945 b1602 b2913 b3915 b3654 b3714 b3664 b0529 b2492 b0904 b1300 b2954 b3029 b1380 b1985 b1518 b0221 b2285 b1007   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.394126 (mmol/gDw/h)
  Minimum Production Rate : 0.597598 (mmol/gDw/h)

Substrate: (mmol/gDw/h)
  EX_o2_e : 39.095039
  EX_glc__D_e : 10.000000
  EX_nh4_e : 7.244507
  EX_pi_e : 0.977773
  EX_so4_e : 0.099249
  EX_k_e : 0.076931
  EX_fe3_e : 0.006332
  EX_mg2_e : 0.003419
  EX_ca2_e : 0.002051
  EX_cl_e : 0.002051
  EX_cu2_e : 0.000279
  EX_mn2_e : 0.000272
  EX_zn2_e : 0.000134
  EX_ni2_e : 0.000127

Product: (mmol/gDw/h)
  EX_h2o_e : 55.421869
  EX_co2_e : 38.443703
  EX_h_e : 6.615699
  Auxiliary production reaction : 0.597597
  EX_mththf_e : 0.000177
  DM_5drib_c : 0.000089
  DM_4crsol_c : 0.000088

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