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 : dctp_c
List of minimal gene deletion strategies (Download)

Gene deletion strategy (36 of 73: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 32
  Gene deletion: b4467 b1478 b4382 b1241 b4069 b4384 b2297 b2458 b2926 b0030 b2407 b3844 b1004 b3713 b1109 b0046 b3236 b0937 b1982 b0261 b0411 b2799 b3945 b1602 b2913 b0529 b2492 b0904 b1380 b0606 b2285 b1010   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.358160 (mmol/gDw/h)
  Minimum Production Rate : 1.126606 (mmol/gDw/h)

 Substrate: (mmol/gDw/h)
  EX_o2_e : 34.156992
  EX_glc__D_e : 10.000000
  EX_nh4_e : 7.249918
  EX_pi_e : 3.725302
  EX_so4_e : 0.090192
  EX_k_e : 0.069910
  EX_fe2_e : 0.005752
  EX_mg2_e : 0.003107
  EX_ca2_e : 0.001864
  EX_cl_e : 0.001864
  EX_cu2_e : 0.000254
  EX_mn2_e : 0.000247
  EX_zn2_e : 0.000122
  EX_ni2_e : 0.000116

Product: (mmol/gDw/h)
  EX_h2o_e : 54.206493
  EX_co2_e : 33.478413
  EX_h_e : 5.258783
  Auxiliary production reaction : 1.126606
  EX_glyclt_e : 0.630742
  EX_ac_e : 0.208516
  EX_ade_e : 0.000401
  DM_5drib_c : 0.000240
  DM_4crsol_c : 0.000080

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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