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 : dcamp_c
List of minimal gene deletion strategies (Download)

Gene deletion strategy (53 of 77: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 34
  Gene deletion: b3399 b3942 b1732 b1241 b0351 b4069 b2744 b1479 b2297 b2458 b3617 b0160 b3236 b2463 b1982 b2210 b0675 b2361 b3551 b4219 b1832 b1778 b4381 b2406 b0114 b0529 b2492 b0904 b1710 b2480 b1517 b0606 b2285 b4209   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.399117 (mmol/gDw/h)
  Minimum Production Rate : 0.754722 (mmol/gDw/h)

 Substrate: (mmol/gDw/h)
  EX_o2_e : 28.575554
  EX_glc__D_e : 10.000000
  EX_nh4_e : 8.126888
  EX_pi_e : 1.139713
  EX_so4_e : 0.100506
  EX_k_e : 0.077905
  EX_mg2_e : 0.003462
  EX_fe2_e : 0.003294
  EX_fe3_e : 0.003116
  EX_ca2_e : 0.002077
  EX_cl_e : 0.002077
  EX_cu2_e : 0.000283
  EX_mn2_e : 0.000276
  EX_zn2_e : 0.000136
  EX_ni2_e : 0.000129

Product: (mmol/gDw/h)
  EX_h2o_e : 49.136830
  EX_co2_e : 25.572497
  EX_h_e : 12.708772
  EX_ac_e : 1.348711
  EX_fum_e : 1.181898
  Auxiliary production reaction : 0.754722
  EX_xan_e : 0.010712
  DM_mththf_c : 0.000179
  DM_5drib_c : 0.000090
  DM_4crsol_c : 0.000089

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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