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 : 12ppd__S_e
List of minimal gene deletion strategies (Download)

Gene deletion strategy (52 of 92: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 32
  Gene deletion: b3553 b1478 b1241 b0351 b2930 b4232 b3697 b3925 b0871 b1004 b3713 b1109 b0046 b3124 b3236 b1779 b2690 b1302 b2662 b1033 b3945 b1602 b4381 b2492 b0904 b1380 b2660 b0514 b1695 b0606 b2285 b4209   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.419283 (mmol/gDw/h)
  Minimum Production Rate : 1.283506 (mmol/gDw/h)

 Substrate: (mmol/gDw/h)
  EX_fe2_e : 1000.000000
  EX_h_e : 994.406035
  EX_o2_e : 282.423172
  EX_glc__D_e : 10.000000
  EX_nh4_e : 4.528217
  EX_pi_e : 0.404443
  EX_so4_e : 0.105584
  EX_k_e : 0.081841
  EX_mg2_e : 0.003637
  EX_cl_e : 0.002182
  EX_ca2_e : 0.002182
  EX_cu2_e : 0.000297
  EX_mn2_e : 0.000290
  EX_zn2_e : 0.000143
  EX_ni2_e : 0.000135
  EX_cobalt2_e : 0.000010

Product: (mmol/gDw/h)
  EX_fe3_e : 999.993266
  EX_h2o_e : 543.520993
  EX_co2_e : 33.735772
  EX_glyc__R_e : 1.734695
  EX_12ppd__S_e : 1.283506
  DM_5drib_c : 0.000094
  DM_4crsol_c : 0.000094

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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