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 : dimp_c
List of minimal gene deletion strategies (Download)

Gene deletion strategy (85 of 85: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 56
  Gene deletion: b3553 b4382 b3942 b1732 b4069 b4384 b3708 b3008 b1479 b3752 b3115 b1849 b2296 b2779 b2925 b2097 b3617 b2407 b3236 b2690 b2463 b3962 b2797 b3117 b1814 b4471 b2210 b4267 b1033 b3551 b2799 b3945 b4219 b1832 b1778 b2239 b2406 b3453 b2868 b0114 b2366 b0306 b3605 b2492 b0904 b2578 b1533 b3927 b2835 b1380 b1710 b2480 b4266 b1517 b0606 b4209   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.407454 (mmol/gDw/h)
  Minimum Production Rate : 0.129629 (mmol/gDw/h)

Substrate: (mmol/gDw/h)
  EX_fe2_e : 1000.000000
  EX_h_e : 990.251204
  EX_o2_e : 279.157133
  EX_glc__D_e : 10.000000
  EX_nh4_e : 4.920082
  EX_pi_e : 0.522662
  EX_so4_e : 0.102605
  EX_k_e : 0.079532
  EX_mg2_e : 0.003535
  EX_ca2_e : 0.002121
  EX_cl_e : 0.002121
  EX_cu2_e : 0.000289
  EX_mn2_e : 0.000282
  EX_zn2_e : 0.000139
  EX_ni2_e : 0.000132
  EX_cobalt2_e : 0.000010

Product: (mmol/gDw/h)
  EX_fe3_e : 999.993456
  EX_h2o_e : 540.017099
  EX_co2_e : 27.147553
  EX_glyc__R_e : 3.872181
  EX_mal__L_e : 0.684697
  EX_ac_e : 0.237214
  Auxiliary production reaction : 0.129629
  EX_hxan_e : 0.000274
  DM_mththf_c : 0.000183
  DM_5drib_c : 0.000092
  DM_4crsol_c : 0.000091

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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