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 : dctp_c
List of minimal gene deletion strategies (Download)

Gene deletion strategy (53 of 73: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 39
  Gene deletion: b3553 b1478 b3399 b4269 b0493 b3588 b3003 b3011 b0474 b1241 b2744 b0871 b2926 b1004 b3713 b1109 b0046 b3236 b1982 b1033 b0675 b2361 b0261 b2799 b3945 b1602 b4381 b3915 b0529 b1539 b2492 b0904 b1380 b2660 b1695 b0606 b2285 b1008 b4209   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.410694 (mmol/gDw/h)
  Minimum Production Rate : 0.705980 (mmol/gDw/h)

Substrate: (mmol/gDw/h)
  EX_o2_e : 35.648315
  EX_glc__D_e : 10.000000
  EX_nh4_e : 7.068612
  EX_pi_e : 2.513776
  EX_so4_e : 0.103422
  EX_k_e : 0.080165
  EX_fe3_e : 0.006598
  EX_mg2_e : 0.003563
  EX_ca2_e : 0.002138
  EX_cl_e : 0.002138
  EX_cu2_e : 0.000291
  EX_mn2_e : 0.000284
  EX_zn2_e : 0.000140
  EX_ni2_e : 0.000133
  EX_cobalt2_e : 0.000010

Product: (mmol/gDw/h)
  EX_h2o_e : 54.735134
  EX_co2_e : 35.557474
  EX_h_e : 5.001624
  Auxiliary production reaction : 0.705873
  EX_hxan_e : 0.089122
  EX_thymd_e : 0.078375
  EX_ade_e : 0.000460
  DM_5drib_c : 0.000276
  DM_4crsol_c : 0.000092

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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