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 : 12ppd__S_e
List of minimal gene deletion strategies (Download)

Gene deletion strategy (43 of 92: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 30
  Gene deletion: b4467 b1478 b3942 b1732 b1241 b0351 b2926 b3844 b1004 b3713 b1109 b0046 b2463 b0937 b2210 b3551 b3945 b1602 b4219 b1832 b1778 b0529 b2492 b0904 b1380 b1710 b2480 b0606 b2285 b1010   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.514431 (mmol/gDw/h)
  Minimum Production Rate : 0.180929 (mmol/gDw/h)

Substrate: (mmol/gDw/h)
  EX_o2_e : 37.063437
  EX_glc__D_e : 10.000000
  EX_nh4_e : 5.555814
  EX_pi_e : 0.496224
  EX_so4_e : 0.129544
  EX_k_e : 0.100413
  EX_fe2_e : 0.008262
  EX_mg2_e : 0.004463
  EX_cl_e : 0.002678
  EX_ca2_e : 0.002678
  EX_cu2_e : 0.000365
  EX_mn2_e : 0.000355
  EX_zn2_e : 0.000175
  EX_ni2_e : 0.000166
  EX_cobalt2_e : 0.000013

Product: (mmol/gDw/h)
  EX_h2o_e : 51.745952
  EX_co2_e : 38.342173
  EX_h_e : 4.726800
  EX_12ppd__S_e : 0.180929
  DM_5drib_c : 0.000116
  DM_4crsol_c : 0.000115

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
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