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 : iasp_c
List of minimal gene deletion strategies (Download)

Gene deletion strategy (8 of 9: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 46
  Gene deletion: b2242 b3553 b4382 b1241 b0351 b4069 b4384 b2297 b2458 b2779 b0030 b2407 b1612 b1611 b4122 b1779 b3962 b0104 b3616 b3589 b4267 b1033 b0675 b1415 b1014 b0822 b3945 b4138 b4123 b0621 b2406 b0112 b0511 b0114 b0529 b2492 b0904 b3028 b3821 b1380 b0325 b0516 b4266 b3662 b1518 b1206   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.329838 (mmol/gDw/h)
  Minimum Production Rate : 0.322276 (mmol/gDw/h)

 Substrate: (mmol/gDw/h)
  EX_fe2_e : 1000.000000
  EX_h_e : 988.616905
  EX_o2_e : 284.788862
  EX_glc__D_e : 10.000000
  EX_nh4_e : 6.414777
  EX_pi_e : 0.318164
  EX_so4_e : 0.083060
  EX_k_e : 0.064382
  EX_mg2_e : 0.002861
  EX_ca2_e : 0.001717
  EX_cl_e : 0.001717
  EX_cu2_e : 0.000234
  EX_mn2_e : 0.000228
  EX_zn2_e : 0.000112
  EX_ni2_e : 0.000107

Product: (mmol/gDw/h)
  EX_fe3_e : 999.994702
  EX_h2o_e : 549.284798
  EX_co2_e : 32.308291
  EX_ac_e : 1.631605
  EX_succ_e : 1.609091
  EX_xan_e : 0.632569
  Auxiliary production reaction : 0.322276
  EX_dxylnt_e : 0.000221
  EX_mththf_e : 0.000148
  DM_5drib_c : 0.000074
  DM_4crsol_c : 0.000074

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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