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 : mal__L_e
List of minimal gene deletion strategies (Download)

Gene deletion strategy (4 of 14: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 34
  Gene deletion: b3553 b1478 b3942 b1732 b1241 b0351 b2779 b3844 b1004 b3713 b1109 b0046 b3236 b2463 b0937 b2210 b1033 b3551 b3945 b1602 b4138 b4123 b0621 b4219 b1832 b1778 b0529 b1380 b1710 b2480 b1206 b0606 b2285 b1007   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.577428 (mmol/gDw/h)
  Minimum Production Rate : 0.599883 (mmol/gDw/h)

 Substrate: (mmol/gDw/h)
  EX_o2_e : 33.044356
  EX_glc__D_e : 10.000000
  EX_nh4_e : 6.236174
  EX_pi_e : 0.556991
  EX_so4_e : 0.145408
  EX_k_e : 0.112710
  EX_fe2_e : 0.009274
  EX_mg2_e : 0.005009
  EX_ca2_e : 0.003006
  EX_cl_e : 0.003006
  EX_cu2_e : 0.000409
  EX_mn2_e : 0.000399
  EX_zn2_e : 0.000197
  EX_ni2_e : 0.000187
  EX_cobalt2_e : 0.000014

Product: (mmol/gDw/h)
  EX_h2o_e : 49.580623
  EX_co2_e : 33.732462
  EX_h_e : 6.533278
  EX_mal__L_e : 0.599883
  EX_hxa_e : 0.027873
  DM_5drib_c : 0.000130
  DM_4crsol_c : 0.000129

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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