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 : datp_c
List of minimal gene deletion strategies (Download)

Gene deletion strategy (114 of 114: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 53
  Gene deletion: b3553 b1478 b3399 b4269 b3942 b1732 b0493 b3588 b3003 b3011 b1241 b4384 b2744 b0871 b2926 b3844 b1004 b3713 b1109 b0046 b3236 b0207 b3012 b1033 b3665 b0675 b2361 b3551 b2799 b1602 b0153 b4219 b1832 b1778 b4381 b3654 b3714 b3664 b0584 b0529 b2492 b0904 b1781 b3001 b1380 b0325 b1710 b2480 b1771 b1518 b0606 b2285 b1011   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.448550 (mmol/gDw/h)
  Minimum Production Rate : 0.375291 (mmol/gDw/h)

Substrate: (mmol/gDw/h)
  EX_o2_e : 36.419906
  EX_glc__D_e : 10.000000
  EX_nh4_e : 6.767700
  EX_pi_e : 1.558546
  EX_so4_e : 0.112954
  EX_k_e : 0.087554
  EX_fe2_e : 0.007204
  EX_mg2_e : 0.003891
  EX_ca2_e : 0.002335
  EX_cl_e : 0.002335
  EX_cu2_e : 0.000318
  EX_mn2_e : 0.000310
  EX_zn2_e : 0.000153
  EX_ni2_e : 0.000145
  EX_cobalt2_e : 0.000011

Product: (mmol/gDw/h)
  EX_h2o_e : 54.037717
  EX_co2_e : 36.833057
  EX_h_e : 5.294273
  EX_acald_e : 0.471721
  Auxiliary production reaction : 0.375291
  EX_hxan_e : 0.011737
  DM_mththf_c : 0.000201
  DM_5drib_c : 0.000101
  DM_4crsol_c : 0.000100

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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