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 : unagamuf_p
List of minimal gene deletion strategies (Download)

Gene deletion strategy (57 of 79: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 31
  Gene deletion: b3399 b0474 b2518 b1241 b0351 b4069 b2744 b4152 b2297 b2458 b2926 b0160 b1612 b1611 b4122 b3616 b3589 b4374 b4161 b0675 b2361 b2291 b4138 b4123 b0621 b0114 b0529 b2492 b0904 b1511 b1206   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.398581 (mmol/gDw/h)
  Minimum Production Rate : 0.091543 (mmol/gDw/h)

 Substrate: (mmol/gDw/h)
  EX_o2_e : 24.686961
  EX_glc__D_e : 10.000000
  EX_nh4_e : 6.737499
  EX_pi_e : 0.567559
  EX_so4_e : 0.100371
  EX_k_e : 0.077800
  EX_fe2_e : 0.006402
  EX_mg2_e : 0.003458
  EX_ca2_e : 0.002075
  EX_cl_e : 0.002075
  EX_cu2_e : 0.000283
  EX_mn2_e : 0.000275
  EX_zn2_e : 0.000136
  EX_ni2_e : 0.000129

Product: (mmol/gDw/h)
  EX_h2o_e : 44.428030
  EX_co2_e : 25.280988
  EX_h_e : 9.408565
  EX_succ_e : 1.212101
  EX_ura_e : 1.079117
  EX_ac_e : 0.980725
  Auxiliary production reaction : 0.091543
  DM_mththf_c : 0.000179
  DM_5drib_c : 0.000090
  DM_4crsol_c : 0.000089

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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