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 (3 of 14: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 34
  Gene deletion: b4467 b1478 b3942 b1732 b1241 b0351 b2779 b1004 b3713 b1109 b0046 b2463 b2210 b3551 b2799 b3945 b1602 b4138 b4123 b0621 b4219 b1832 b1778 b3915 b0452 b0529 b1380 b1710 b2480 b1206 b0606 b2285 b1011 b4209   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.569376 (mmol/gDw/h)
  Minimum Production Rate : 0.731551 (mmol/gDw/h)

 Substrate: (mmol/gDw/h)
  EX_o2_e : 33.217740
  EX_glc__D_e : 10.000000
  EX_nh4_e : 6.149210
  EX_pi_e : 0.549223
  EX_so4_e : 0.143380
  EX_k_e : 0.111138
  EX_fe3_e : 0.009145
  EX_mg2_e : 0.004939
  EX_cl_e : 0.002964
  EX_ca2_e : 0.002964
  EX_cu2_e : 0.000404
  EX_mn2_e : 0.000393
  EX_zn2_e : 0.000194
  EX_ni2_e : 0.000184
  EX_cobalt2_e : 0.000014

Product: (mmol/gDw/h)
  EX_h2o_e : 49.466154
  EX_co2_e : 33.703535
  EX_h_e : 6.703899
  EX_mal__L_e : 0.731551
  DM_5drib_c : 0.000128
  DM_4crsol_c : 0.000127

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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