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 : hxan_e
List of minimal gene deletion strategies (Download)

Gene deletion strategy (62 of 78: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 26
  Gene deletion: b3553 b4382 b0238 b0125 b4384 b0871 b1004 b3713 b1109 b0046 b2883 b0477 b2210 b1033 b1602 b2913 b2868 b0114 b0755 b3612 b0529 b2492 b0904 b1380 b1511 b2285   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.505741 (mmol/gDw/h)
  Minimum Production Rate : 0.081535 (mmol/gDw/h)

 Substrate: (mmol/gDw/h)
  EX_o2_e : 37.957437
  EX_glc__D_e : 10.000000
  EX_nh4_e : 5.788097
  EX_pi_e : 0.487840
  EX_so4_e : 0.127356
  EX_k_e : 0.098717
  EX_fe2_e : 0.008123
  EX_mg2_e : 0.004387
  EX_ca2_e : 0.002632
  EX_cl_e : 0.002632
  EX_cu2_e : 0.000359
  EX_mn2_e : 0.000349
  EX_zn2_e : 0.000172
  EX_ni2_e : 0.000163
  EX_cobalt2_e : 0.000013

Product: (mmol/gDw/h)
  EX_h2o_e : 52.921890
  EX_co2_e : 38.832860
  EX_h_e : 4.973088
  EX_hxan_e : 0.081535
  DM_mththf_c : 0.000227
  DM_5drib_c : 0.000114
  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
Contact