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 : sbt6p_c
List of minimal gene deletion strategies (Download)

Gene deletion strategy (77 of 83: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 46
  Gene deletion: b3553 b1478 b4269 b3942 b1732 b0493 b3588 b3003 b3011 b1241 b0351 b0871 b2779 b1004 b3713 b1109 b0046 b3236 b2463 b0207 b3012 b2210 b1033 b3551 b2799 b1602 b4219 b1832 b1778 b3915 b0529 b2492 b0904 b1781 b3001 b3821 b1380 b0325 b1710 b2480 b1695 b1771 b0606 b2285 b1011 b4209   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.462093 (mmol/gDw/h)
  Minimum Production Rate : 0.111844 (mmol/gDw/h)

Substrate: (mmol/gDw/h)
  EX_fe2_e : 1000.000000
  EX_h_e : 994.782947
  EX_o2_e : 286.856145
  EX_glc__D_e : 10.000000
  EX_nh4_e : 4.990568
  EX_pi_e : 0.557582
  EX_so4_e : 0.116364
  EX_k_e : 0.090197
  EX_mg2_e : 0.004009
  EX_cl_e : 0.002405
  EX_ca2_e : 0.002405
  EX_cu2_e : 0.000328
  EX_mn2_e : 0.000319
  EX_zn2_e : 0.000158
  EX_ni2_e : 0.000149
  EX_cobalt2_e : 0.000012

Product: (mmol/gDw/h)
  EX_fe3_e : 999.992578
  EX_h2o_e : 550.784098
  EX_co2_e : 37.621470
  EX_fum_e : 0.481867
  EX_acald_e : 0.406597
  Auxiliary production reaction : 0.111844
  DM_5drib_c : 0.000104
  DM_4crsol_c : 0.000103

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