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 : dcyt_c
List of minimal gene deletion strategies (Download)

Gene deletion strategy (36 of 41: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 44
  Gene deletion: b3553 b1478 b3942 b1732 b1241 b4069 b4384 b3115 b1849 b2296 b2926 b0030 b2407 b1004 b3713 b1109 b0046 b3236 b2463 b1982 b2210 b1033 b3551 b0411 b2799 b3945 b1602 b4219 b1832 b1778 b4381 b3915 b0452 b0529 b2492 b0904 b1380 b1710 b2480 b1511 b0606 b2285 b1009 b4209   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.360295 (mmol/gDw/h)
  Minimum Production Rate : 1.186308 (mmol/gDw/h)

Substrate: (mmol/gDw/h)
  EX_o2_e : 33.157033
  EX_glc__D_e : 10.000000
  EX_nh4_e : 7.451049
  EX_pi_e : 0.347543
  EX_so4_e : 0.090730
  EX_k_e : 0.070327
  EX_fe3_e : 0.005787
  EX_mg2_e : 0.003126
  EX_ca2_e : 0.001875
  EX_cl_e : 0.001875
  EX_cu2_e : 0.000255
  EX_mn2_e : 0.000249
  EX_zn2_e : 0.000123
  EX_ni2_e : 0.000116

Product: (mmol/gDw/h)
  EX_h2o_e : 50.558282
  EX_co2_e : 32.364245
  EX_h_e : 7.960469
  Auxiliary production reaction : 1.186308
  EX_mal__L_e : 0.376198
  EX_ac_e : 0.331859
  EX_hxan_e : 0.000242
  EX_mththf_e : 0.000161
  DM_5drib_c : 0.000081
  DM_4crsol_c : 0.000080

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.

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Last updated: 21-Sep-2023
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