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 : glyclt_c
List of minimal gene deletion strategies (Download)

Gene deletion strategy (46 of 83: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 30
  Gene deletion: b4467 b3403 b1479 b2779 b2925 b2097 b1850 b1004 b3713 b1109 b0046 b3236 b2690 b2463 b0675 b1493 b3517 b0822 b0726 b1602 b0507 b2913 b1727 b2975 b3603 b1380 b0118 b1695 b2285 b3924   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.544004 (mmol/gDw/h)
  Minimum Production Rate : 0.513153 (mmol/gDw/h)

Substrate: (mmol/gDw/h)
  EX_o2_e : 35.740472
  EX_glc__D_e : 10.000000
  EX_nh4_e : 5.875201
  EX_pi_e : 0.524750
  EX_so4_e : 0.136991
  EX_k_e : 0.106186
  EX_fe2_e : 0.008737
  EX_mg2_e : 0.004719
  EX_ca2_e : 0.002832
  EX_cl_e : 0.002832
  EX_cu2_e : 0.000386
  EX_mn2_e : 0.000376
  EX_zn2_e : 0.000186
  EX_ni2_e : 0.000176
  EX_cobalt2_e : 0.000014

Product: (mmol/gDw/h)
  EX_h2o_e : 51.010464
  EX_co2_e : 36.644812
  EX_h_e : 5.511683
  Auxiliary production reaction : 0.513153
  DM_5drib_c : 0.000122
  DM_4crsol_c : 0.000121

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