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 : 2p4c2me_c
List of minimal gene deletion strategies (Download)

Gene deletion strategy (116 of 116: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 74
  Gene deletion: b2836 b2242 b3553 b3399 b0586 b0474 b2518 b1241 b0351 b3831 b4069 b2744 b3708 b1479 b3752 b2297 b2458 b2925 b2097 b2926 b2781 b0160 b3236 b1612 b1611 b0517 b4122 b2690 b1759 b3962 b0104 b2797 b3117 b1814 b4471 b3616 b3589 b2210 b4267 b1033 b4161 b0675 b2361 b1415 b1014 b0261 b0505 b3945 b1907 b4138 b4123 b0621 b4381 b2406 b0112 b0511 b4265 b0114 b2366 b0755 b3612 b2492 b0904 b1533 b3927 b3028 b1380 b3918 b0325 b4042 b1473 b0494 b4266 b1206   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.276708 (mmol/gDw/h)
  Minimum Production Rate : 0.295742 (mmol/gDw/h)

Substrate: (mmol/gDw/h)
  EX_fe2_e : 1000.000000
  EX_h_e : 989.113306
  EX_o2_e : 280.839003
  EX_glc__D_e : 10.000000
  EX_nh4_e : 5.532923
  EX_pi_e : 1.154140
  EX_so4_e : 0.069681
  EX_k_e : 0.054012
  EX_mg2_e : 0.002400
  EX_cl_e : 0.001440
  EX_ca2_e : 0.001440
  EX_cu2_e : 0.000196
  EX_mn2_e : 0.000191
  EX_zn2_e : 0.000094
  EX_ni2_e : 0.000089

Product: (mmol/gDw/h)
  EX_fe3_e : 999.995556
  EX_h2o_e : 544.614492
  EX_co2_e : 29.531191
  EX_ac_e : 4.252345
  EX_succ_e : 1.067100
  EX_xan_e : 0.389275
  Auxiliary production reaction : 0.295742
  EX_thym_e : 0.050085
  EX_dxylnt_e : 0.000185
  DM_5drib_c : 0.000062
  DM_4crsol_c : 0.000062

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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