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 : udpg_c
List of minimal gene deletion strategies (Download)

Gene deletion strategy (83 of 83: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 63
  Gene deletion: b2242 b3553 b1478 b3399 b1241 b0351 b4069 b2502 b2744 b1278 b3708 b3614 b0910 b2297 b2458 b2779 b2781 b1612 b1611 b4122 b0907 b1759 b3962 b0104 b2797 b3117 b1814 b4471 b3616 b3589 b4267 b1033 b4374 b0675 b2361 b2291 b1415 b1014 b3945 b1907 b4138 b4123 b0621 b0112 b0511 b0114 b1539 b2492 b0904 b3035 b1533 b3028 b3821 b1380 b3918 b0325 b0508 b1473 b0516 b4266 b2842 b1518 b1206   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.317712 (mmol/gDw/h)
  Minimum Production Rate : 0.368532 (mmol/gDw/h)

Substrate: (mmol/gDw/h)
  EX_o2_e : 33.305000
  EX_glc__D_e : 10.000000
  EX_nh4_e : 6.186476
  EX_pi_e : 1.043531
  EX_so4_e : 0.080006
  EX_k_e : 0.062015
  EX_fe2_e : 0.005103
  EX_mg2_e : 0.002756
  EX_ca2_e : 0.001654
  EX_cl_e : 0.001654
  EX_cu2_e : 0.000225
  EX_mn2_e : 0.000220
  EX_zn2_e : 0.000108
  EX_ni2_e : 0.000103

Product: (mmol/gDw/h)
  EX_h2o_e : 48.834234
  EX_co2_e : 31.275084
  EX_h_e : 8.710531
  EX_succ_e : 1.282876
  EX_ac_e : 1.207223
  EX_xan_e : 0.475784
  Auxiliary production reaction : 0.368532
  EX_ura_e : 0.057507
  DM_mththf_c : 0.000142
  EX_dxylnt_e : 0.000142
  DM_5drib_c : 0.000071
  DM_4crsol_c : 0.000071

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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