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 : nadhx__R_c
List of minimal gene deletion strategies (Download)

Gene deletion strategy (112 of 116: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 46
  Gene deletion: b4467 b1478 b3399 b4269 b3942 b1732 b0493 b3588 b3003 b3011 b1241 b0351 b2744 b0871 b2779 b3617 b0160 b3844 b1004 b3713 b1109 b0046 b2463 b0937 b1982 b2210 b4374 b0675 b2361 b2291 b3551 b0261 b1602 b4219 b1832 b1778 b0114 b0529 b2492 b0904 b1380 b1710 b2480 b1771 b0606 b2285   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.315073 (mmol/gDw/h)
  Minimum Production Rate : 0.512114 (mmol/gDw/h)

Substrate: (mmol/gDw/h)
  EX_o2_e : 33.639443
  EX_glc__D_e : 10.000000
  EX_nh4_e : 6.988977
  EX_pi_e : 1.328150
  EX_so4_e : 0.079342
  EX_k_e : 0.061500
  EX_fe2_e : 0.005060
  EX_mg2_e : 0.002733
  EX_ca2_e : 0.001640
  EX_cl_e : 0.001640
  EX_cu2_e : 0.000223
  EX_mn2_e : 0.000218
  EX_zn2_e : 0.000107
  EX_ni2_e : 0.000102

Product: (mmol/gDw/h)
  EX_h2o_e : 51.479134
  EX_co2_e : 33.425570
  EX_h_e : 5.892284
  EX_acald_e : 0.789701
  Auxiliary production reaction : 0.512114
  EX_3hpp_e : 0.435282
  EX_hxan_e : 0.000353
  DM_5drib_c : 0.000211
  DM_4crsol_c : 0.000070

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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