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 : 2p4c2me_c
List of minimal gene deletion strategies (Download)

Gene deletion strategy (115 of 116: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 71
  Gene deletion: b4467 b2242 b0586 b0474 b2518 b1241 b0351 b4069 b2744 b3708 b3115 b1849 b2296 b2781 b0099 b0160 b1612 b1611 b2883 b4122 b0907 b1759 b3962 b0104 b2797 b3117 b1814 b4471 b3616 b3589 b4267 b4374 b4161 b0675 b2361 b2291 b1415 b1014 b2799 b3945 b3709 b1907 b4138 b4123 b0621 b3161 b0112 b2868 b4265 b4064 b4464 b0114 b2366 b0755 b3612 b2492 b0904 b1533 b3927 b3028 b3821 b1380 b3918 b0508 b4042 b1473 b1511 b4266 b3662 b1813 b1206   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.271192 (mmol/gDw/h)
  Minimum Production Rate : 0.720689 (mmol/gDw/h)

Substrate: (mmol/gDw/h)
  EX_o2_e : 31.731164
  EX_glc__D_e : 10.000000
  EX_nh4_e : 5.189086
  EX_pi_e : 2.423660
  EX_so4_e : 0.068291
  EX_k_e : 0.052935
  EX_fe2_e : 0.004356
  EX_mg2_e : 0.002353
  EX_ca2_e : 0.001412
  EX_cl_e : 0.001412
  EX_cu2_e : 0.000192
  EX_mn2_e : 0.000187
  EX_zn2_e : 0.000092
  EX_ni2_e : 0.000088

Product: (mmol/gDw/h)
  EX_h2o_e : 47.037117
  EX_co2_e : 31.328342
  EX_h_e : 6.937442
  EX_ac_e : 1.436576
  EX_succ_e : 1.095033
  Auxiliary production reaction : 0.720689
  EX_ura_e : 0.049086
  DM_mththf_c : 0.000121
  EX_dxylnt_e : 0.000121
  DM_5drib_c : 0.000061
  DM_4crsol_c : 0.000060

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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