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 : imacp_c
List of minimal gene deletion strategies (Download)

Gene deletion strategy (100 of 103: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 46
  Gene deletion: b4467 b1478 b3942 b1732 b1241 b0351 b4069 b4384 b2744 b3708 b3614 b0910 b2297 b2458 b3617 b0030 b2407 b3844 b1004 b3713 b1109 b0046 b3236 b1779 b1982 b2797 b3117 b1814 b4471 b4374 b0675 b0411 b1602 b0507 b4381 b2406 b0114 b1539 b2492 b0904 b1533 b1380 b1511 b0606 b0221 b2285   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.393731 (mmol/gDw/h)
  Minimum Production Rate : 0.075886 (mmol/gDw/h)

 Substrate: (mmol/gDw/h)
  EX_fe2_e : 1000.000000
  EX_h_e : 993.283836
  EX_o2_e : 285.411254
  EX_glc__D_e : 10.000000
  EX_nh4_e : 6.091636
  EX_pi_e : 1.141697
  EX_so4_e : 0.099149
  EX_k_e : 0.076853
  EX_mg2_e : 0.003416
  EX_ca2_e : 0.002049
  EX_cl_e : 0.002049
  EX_cu2_e : 0.000279
  EX_mn2_e : 0.000272
  EX_zn2_e : 0.000134
  EX_ni2_e : 0.000127

Product: (mmol/gDw/h)
  EX_fe3_e : 999.993676
  EX_h2o_e : 551.209244
  EX_co2_e : 35.541242
  EX_ac_e : 1.079404
  Auxiliary production reaction : 0.761901
  DM_oxam_c : 0.173041
  EX_mththf_e : 0.172777
  EX_thym_e : 0.071266
  DM_5drib_c : 0.000264
  EX_glyclt_e : 0.000263
  DM_4crsol_c : 0.000088

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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