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 : nadp_c
List of minimal gene deletion strategies (Download)

Gene deletion strategy (61 of 74: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 41
  Gene deletion: b3553 b1478 b3846 b1241 b4069 b4384 b3115 b1849 b2296 b2926 b0030 b2407 b1004 b3713 b1109 b0046 b3236 b1638 b1982 b0477 b4139 b1033 b0261 b2799 b3945 b1602 b2913 b4381 b2406 b3915 b0509 b3125 b0529 b2492 b0904 b2954 b3029 b1380 b3662 b2285 b1007   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.489660 (mmol/gDw/h)
  Minimum Production Rate : 0.049960 (mmol/gDw/h)

 Substrate: (mmol/gDw/h)
  EX_o2_e : 37.382801
  EX_glc__D_e : 10.000000
  EX_nh4_e : 5.640746
  EX_pi_e : 0.622210
  EX_so4_e : 0.123306
  EX_k_e : 0.095578
  EX_fe3_e : 0.007864
  EX_mg2_e : 0.004248
  EX_ca2_e : 0.002549
  EX_cl_e : 0.002549
  EX_cu2_e : 0.000347
  EX_mn2_e : 0.000338
  EX_zn2_e : 0.000167
  EX_ni2_e : 0.000158
  EX_cobalt2_e : 0.000012

Product: (mmol/gDw/h)
  EX_h2o_e : 52.309805
  EX_co2_e : 38.278570
  EX_h_e : 4.994708
  EX_ac_e : 0.285073
  Auxiliary production reaction : 0.049960
  EX_ade_e : 0.000548
  DM_5drib_c : 0.000329
  DM_4crsol_c : 0.000109

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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