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 : ins_c
List of minimal gene deletion strategies (Download)

Gene deletion strategy (38 of 38: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 48
  Gene deletion: b4382 b3942 b1732 b0474 b2518 b4069 b4384 b3708 b1479 b3752 b2930 b4232 b3697 b3925 b2297 b2458 b2407 b3236 b1779 b2690 b2463 b2797 b3117 b1814 b4471 b3449 b2210 b3665 b3551 b3945 b4219 b1832 b1778 b2239 b2406 b0114 b2366 b0529 b2492 b0904 b1533 b3927 b1710 b2480 b1511 b0606 b2285 b4209   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.374329 (mmol/gDw/h)
  Minimum Production Rate : 0.158788 (mmol/gDw/h)

 Substrate: (mmol/gDw/h)
  EX_o2_e : 31.738703
  EX_glc__D_e : 10.000000
  EX_nh4_e : 4.679130
  EX_pi_e : 0.361080
  EX_so4_e : 0.094263
  EX_k_e : 0.073066
  EX_mg2_e : 0.003247
  EX_fe2_e : 0.003089
  EX_fe3_e : 0.002923
  EX_ca2_e : 0.001948
  EX_cl_e : 0.001948
  EX_cu2_e : 0.000265
  EX_mn2_e : 0.000259
  EX_zn2_e : 0.000128
  EX_ni2_e : 0.000121

Product: (mmol/gDw/h)
  EX_h2o_e : 43.614584
  EX_co2_e : 31.591022
  EX_h_e : 9.806078
  EX_ac_e : 4.627985
  EX_mal__L_e : 0.549639
  Auxiliary production reaction : 0.158788
  EX_ade_e : 0.000252
  DM_mththf_c : 0.000168
  DM_5drib_c : 0.000084
  DM_4crsol_c : 0.000083

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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