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 : 5mthf_c
List of minimal gene deletion strategies (Download)

Gene deletion strategy (120 of 120: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 77
  Gene deletion: b3553 b1478 b4269 b0493 b3588 b3003 b3011 b0474 b2518 b1241 b0351 b4069 b4384 b2744 b1278 b3708 b1479 b2930 b4232 b3697 b3925 b0871 b2297 b2458 b0030 b2407 b3236 b0907 b2690 b0120 b3962 b1982 b0104 b2797 b3117 b1814 b4471 b3616 b3589 b4267 b1033 b0595 b4374 b0675 b2361 b2291 b1415 b1014 b4014 b0261 b2976 b0411 b0822 b0507 b3709 b1907 b3161 b0112 b0837 b0124 b0114 b0755 b3612 b1539 b2492 b0904 b1533 b2835 b1380 b0325 b2413 b1473 b0494 b3715 b4266 b3662 b1813   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.189302 (mmol/gDw/h)
  Minimum Production Rate : 0.401946 (mmol/gDw/h)

Substrate: (mmol/gDw/h)
  EX_o2_e : 28.610255
  EX_glc__D_e : 10.000000
  EX_nh4_e : 5.022795
  EX_so4_e : 0.212188
  EX_pi_e : 0.182602
  EX_k_e : 0.036950
  EX_fe2_e : 0.003040
  EX_mg2_e : 0.001642
  EX_cl_e : 0.000985
  EX_ca2_e : 0.000985
  EX_cu2_e : 0.000134
  EX_mn2_e : 0.000131
  EX_zn2_e : 0.000065
  EX_ni2_e : 0.000061

Product: (mmol/gDw/h)
  EX_h2o_e : 43.461312
  EX_co2_e : 26.835078
  EX_h_e : 9.530420
  EX_pyr_e : 4.062810
  EX_acald_e : 0.892280
  EX_dxylnt_e : 0.402030
  Auxiliary production reaction : 0.401946
  EX_ac_e : 0.274727
  EX_met__L_e : 0.164518
  DM_oxam_c : 0.000212
  DM_5drib_c : 0.000127
  DM_4crsol_c : 0.000042

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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