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 (34 of 77: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 25
  Gene deletion: b4382 b1241 b0351 b4069 b4384 b2744 b2297 b2458 b2925 b2097 b0030 b2407 b2690 b1982 b3616 b3589 b0261 b0411 b3945 b0114 b0529 b2492 b0904 b3662 b2285   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.425331 (mmol/gDw/h)
  Minimum Production Rate : 0.418610 (mmol/gDw/h)

 Substrate: (mmol/gDw/h)
  EX_o2_e : 27.449475
  EX_glc__D_e : 10.000000
  EX_nh4_e : 8.273162
  EX_pi_e : 0.828886
  EX_so4_e : 0.107107
  EX_k_e : 0.083022
  EX_fe2_e : 0.006831
  EX_mg2_e : 0.003690
  EX_ca2_e : 0.002214
  EX_cl_e : 0.002214
  EX_cu2_e : 0.000302
  EX_mn2_e : 0.000294
  EX_zn2_e : 0.000145
  EX_ni2_e : 0.000137
  EX_cobalt2_e : 0.000011

Product: (mmol/gDw/h)
  EX_h2o_e : 48.346462
  EX_co2_e : 26.494861
  EX_h_e : 9.552592
  EX_ac_e : 1.127161
  EX_thymd_e : 0.793051
  Auxiliary production reaction : 0.418610
  DM_oxam_c : 0.000476
  DM_5drib_c : 0.000285
  DM_4crsol_c : 0.000095

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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