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 : mnl1p_c
List of minimal gene deletion strategies (Download)

Gene deletion strategy (28 of 80: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 35
  Gene deletion: b4467 b1478 b4382 b3942 b1732 b1241 b0351 b4384 b0871 b2779 b2925 b2097 b2407 b3844 b1004 b3713 b1109 b0046 b3236 b2690 b2210 b2799 b3945 b1602 b3915 b0529 b1539 b2492 b0904 b3927 b1380 b2660 b0606 b2285 b1008   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.374141 (mmol/gDw/h)
  Minimum Production Rate : 0.041235 (mmol/gDw/h)

 Substrate: (mmol/gDw/h)
  EX_o2_e : 30.383819
  EX_glc__D_e : 10.000000
  EX_nh4_e : 4.040686
  EX_pi_e : 0.402134
  EX_so4_e : 0.094216
  EX_k_e : 0.073030
  EX_fe3_e : 0.006009
  EX_mg2_e : 0.003246
  EX_ca2_e : 0.001947
  EX_cl_e : 0.001947
  EX_cu2_e : 0.000265
  EX_mn2_e : 0.000259
  EX_zn2_e : 0.000128
  EX_ni2_e : 0.000121

Product: (mmol/gDw/h)
  EX_h2o_e : 43.719670
  EX_co2_e : 28.566068
  EX_h_e : 8.720352
  EX_pyr_e : 5.276590
  Auxiliary production reaction : 0.041235
  DM_5drib_c : 0.000084
  DM_4crsol_c : 0.000083

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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