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 : mal__L_c
List of minimal gene deletion strategies (Download)

Gene deletion strategy (20 of 29: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 35
  Gene deletion: b3553 b1478 b3942 b1732 b1241 b0351 b3844 b1004 b3713 b1109 b0046 b2463 b2210 b1033 b3551 b2799 b3945 b1602 b0153 b4219 b1832 b1778 b0590 b0755 b3612 b0529 b2492 b0904 b1380 b1710 b2480 b1206 b0606 b2285 b1011   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.503172 (mmol/gDw/h)
  Minimum Production Rate : 0.571317 (mmol/gDw/h)

Substrate: (mmol/gDw/h)
  EX_o2_e : 36.559368
  EX_glc__D_e : 10.000000
  EX_nh4_e : 5.434216
  EX_pi_e : 0.485363
  EX_so4_e : 0.126709
  EX_k_e : 0.098216
  EX_fe2_e : 0.008081
  EX_mg2_e : 0.004365
  EX_cl_e : 0.002619
  EX_ca2_e : 0.002619
  EX_cu2_e : 0.000357
  EX_mn2_e : 0.000348
  EX_zn2_e : 0.000172
  EX_ni2_e : 0.000163
  EX_cobalt2_e : 0.000013

Product: (mmol/gDw/h)
  EX_h2o_e : 50.920531
  EX_co2_e : 37.061831
  EX_h_e : 5.765979
  Auxiliary production reaction : 0.571317
  DM_5drib_c : 0.000113
  DM_4crsol_c : 0.000112

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.

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Last updated: 21-Sep-2023
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