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 : ametam_c
List of minimal gene deletion strategies (Download)

Gene deletion strategy (84 of 84: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 53
  Gene deletion: b4467 b1478 b3399 b4269 b0493 b3588 b3003 b3011 b1241 b2744 b3708 b3008 b0871 b2926 b3844 b1004 b3713 b1109 b0046 b3236 b2883 b1638 b2920 b1982 b1302 b2662 b4139 b2797 b3117 b1814 b4471 b0675 b2361 b2291 b4015 b0261 b2799 b3945 b1602 b0153 b2913 b4381 b0584 b0728 b2366 b2492 b0904 b2954 b1533 b3029 b1380 b2285 b1011   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.504369 (mmol/gDw/h)
  Minimum Production Rate : 0.035048 (mmol/gDw/h)

 Substrate: (mmol/gDw/h)
  EX_o2_e : 37.692827
  EX_glc__D_e : 10.000000
  EX_nh4_e : 5.657437
  EX_pi_e : 0.486518
  EX_so4_e : 0.162059
  EX_k_e : 0.098449
  EX_mg2_e : 0.004375
  EX_fe2_e : 0.004163
  EX_fe3_e : 0.003938
  EX_ca2_e : 0.002625
  EX_cl_e : 0.002625
  EX_cu2_e : 0.000358
  EX_mn2_e : 0.000349
  EX_zn2_e : 0.000172
  EX_ni2_e : 0.000163
  EX_cobalt2_e : 0.000013

Product: (mmol/gDw/h)
  EX_h2o_e : 52.577685
  EX_co2_e : 38.805024
  EX_h_e : 4.708946
  Auxiliary production reaction : 0.035048
  EX_glyclt_e : 0.000564
  DM_5drib_c : 0.000338
  DM_4crsol_c : 0.000112

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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