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 : nadh_c
List of minimal gene deletion strategies (Download)

Gene deletion strategy (64 of 81: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 39
  Gene deletion: b3553 b1478 b3942 b1732 b3794 b1241 b0351 b4069 b3708 b2779 b3844 b1004 b3713 b1109 b0046 b3236 b1033 b3551 b0335 b2799 b3945 b1602 b0507 b4219 b1832 b1778 b3915 b0728 b0529 b2835 b1380 b1710 b2480 b0494 b3546 b0606 b0221 b2285 b1010   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.591842 (mmol/gDw/h)
  Minimum Production Rate : 0.019597 (mmol/gDw/h)

Substrate: (mmol/gDw/h)
  EX_o2_e : 34.079677
  EX_glc__D_e : 10.000000
  EX_nh4_e : 6.529024
  EX_pi_e : 0.610089
  EX_so4_e : 0.149038
  EX_k_e : 0.115523
  EX_fe3_e : 0.009506
  EX_mg2_e : 0.005134
  EX_ca2_e : 0.003081
  EX_cl_e : 0.003081
  EX_cu2_e : 0.000420
  EX_mn2_e : 0.000409
  EX_zn2_e : 0.000202
  EX_ni2_e : 0.000191
  EX_cobalt2_e : 0.000015

Product: (mmol/gDw/h)
  EX_h2o_e : 51.312166
  EX_co2_e : 35.296062
  EX_h_e : 5.545572
  Auxiliary production reaction : 0.019597
  DM_5drib_c : 0.000133
  DM_4crsol_c : 0.000132

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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