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 : pnto__R_c
List of minimal gene deletion strategies (Download)

Gene deletion strategy (57 of 79: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 38
  Gene deletion: b1478 b4382 b0474 b2518 b1241 b4384 b3708 b3008 b0910 b3752 b0871 b2925 b2097 b2407 b3236 b2690 b1982 b2797 b3117 b1814 b4471 b2210 b2440 b3665 b0675 b0822 b2406 b0114 b0886 b1539 b2492 b0904 b2578 b1533 b3927 b2413 b3662 b1517   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.765277 (mmol/gDw/h)
  Minimum Production Rate : 0.108619 (mmol/gDw/h)

 Substrate: (mmol/gDw/h)
  EX_fe2_e : 1000.000000
  EX_h_e : 992.036684
  EX_o2_e : 274.814017
  EX_glc__D_e : 10.000000
  EX_nh4_e : 9.075662
  EX_pi_e : 0.738191
  EX_so4_e : 0.192712
  EX_k_e : 0.149377
  EX_mg2_e : 0.006639
  EX_cl_e : 0.003983
  EX_ca2_e : 0.003983
  EX_cu2_e : 0.000543
  EX_mn2_e : 0.000529
  EX_zn2_e : 0.000261
  EX_ni2_e : 0.000247
  EX_cobalt2_e : 0.000019

Product: (mmol/gDw/h)
  EX_fe3_e : 999.987709
  EX_h2o_e : 548.032118
  EX_co2_e : 26.207941
  EX_ade_e : 0.140422
  DM_mththf_c : 0.139909
  Auxiliary production reaction : 0.108619
  DM_5drib_c : 0.000514
  DM_4crsol_c : 0.000171

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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