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 : dcmp_c
List of minimal gene deletion strategies (Download)

Gene deletion strategy (52 of 117: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 33
  Gene deletion: b3399 b3942 b1732 b1241 b0351 b4069 b2502 b2744 b1479 b2297 b2458 b3617 b1238 b3236 b2463 b1982 b2210 b0675 b2361 b3551 b0261 b4219 b1832 b1778 b4381 b0114 b0529 b2492 b0904 b1710 b2480 b0606 b4209   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.508440 (mmol/gDw/h)
  Minimum Production Rate : 1.501217 (mmol/gDw/h)

 Substrate: (mmol/gDw/h)
  EX_o2_e : 19.594476
  EX_nh4_e : 10.892244
  EX_glc__D_e : 10.000000
  EX_pi_e : 1.991661
  EX_so4_e : 0.128035
  EX_k_e : 0.099244
  EX_mg2_e : 0.004411
  EX_fe2_e : 0.004196
  EX_fe3_e : 0.003970
  EX_ca2_e : 0.002646
  EX_cl_e : 0.002646
  EX_cu2_e : 0.000360
  EX_mn2_e : 0.000351
  EX_zn2_e : 0.000173
  EX_ni2_e : 0.000164
  EX_cobalt2_e : 0.000013

Product: (mmol/gDw/h)
  EX_h2o_e : 47.078870
  EX_co2_e : 18.422542
  EX_h_e : 11.435532
  Auxiliary production reaction : 1.501217
  EX_mal__L_e : 0.531335
  EX_thymd_e : 0.447606
  EX_ac_e : 0.296007
  EX_xan_e : 0.000569
  DM_5drib_c : 0.000341
  DM_4crsol_c : 0.000113

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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