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 : ipdp_c
List of minimal gene deletion strategies (Download)

Gene deletion strategy (45 of 77: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 25
  Gene deletion: b3831 b2744 b3614 b0910 b4152 b2781 b0030 b1612 b1611 b4122 b0651 b2162 b1759 b4374 b2361 b2291 b4138 b4123 b0621 b2406 b3825 b3918 b4042 b0494 b1206   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.726228 (mmol/gDw/h)
  Minimum Production Rate : 0.383554 (mmol/gDw/h)

Substrate: (mmol/gDw/h)
  EX_fe2_e : 1000.000000
  EX_h_e : 991.154400
  EX_o2_e : 272.016021
  EX_glc__D_e : 10.000000
  EX_nh4_e : 8.873208
  EX_pi_e : 1.467631
  EX_so4_e : 0.182879
  EX_k_e : 0.141755
  EX_mg2_e : 0.006300
  EX_cl_e : 0.003780
  EX_ca2_e : 0.003780
  EX_cu2_e : 0.000515
  EX_mn2_e : 0.000502
  EX_zn2_e : 0.000248
  EX_ni2_e : 0.000235
  EX_cobalt2_e : 0.000018

Product: (mmol/gDw/h)
  EX_fe3_e : 999.988336
  EX_h2o_e : 546.455945
  EX_co2_e : 23.184673
  EX_succ_e : 0.757305
  EX_ura_e : 0.515003
  Auxiliary production reaction : 0.383554
  DM_5drib_c : 0.000163
  DM_4crsol_c : 0.000162

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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