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 : 4ppan_c
List of minimal gene deletion strategies (Download)

Gene deletion strategy (63 of 88: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 40
  Gene deletion: b3553 b1478 b3399 b4382 b0474 b2518 b1241 b0351 b4069 b2744 b3708 b0871 b2297 b2458 b2779 b2925 b2097 b3617 b0160 b0517 b2690 b1982 b2797 b3117 b1814 b4471 b1033 b0675 b2361 b0822 b4381 b2406 b0114 b2366 b2492 b0904 b1533 b1912 b0508 b1511   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.523110 (mmol/gDw/h)
  Minimum Production Rate : 0.362786 (mmol/gDw/h)

 Substrate: (mmol/gDw/h)
  EX_o2_e : 26.628810
  EX_glc__D_e : 10.000000
  EX_nh4_e : 8.420250
  EX_pi_e : 0.867380
  EX_so4_e : 0.131729
  EX_k_e : 0.102107
  EX_fe2_e : 0.008402
  EX_mg2_e : 0.004538
  EX_ca2_e : 0.002723
  EX_cl_e : 0.002723
  EX_cu2_e : 0.000371
  EX_mn2_e : 0.000361
  EX_zn2_e : 0.000178
  EX_ni2_e : 0.000169
  EX_cobalt2_e : 0.000013

Product: (mmol/gDw/h)
  EX_h2o_e : 45.418113
  EX_co2_e : 26.302008
  EX_h_e : 9.746383
  EX_ac_e : 1.806172
  EX_alltn_e : 0.601981
  DM_mththf_c : 0.587942
  Auxiliary production reaction : 0.362786
  DM_5drib_c : 0.000351
  EX_glyc__R_e : 0.000175
  DM_4crsol_c : 0.000117

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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