MetNetComp Database [1] / Minimal gene deletions

Minimal gene deletions for simulation-based growth-coupled production. You can also see maximal gene deletions.

Model : STM_v1_0 [2].
Target metabolite : ddca_p
List of minimal gene deletion strategies (Download)

Gene deletion strategy (50 of 113: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 36
  Gene deletion: STM1463 STM1749 STM2463 STM2285 STM3526 STM1290 STM4567 STM4326 STM1511 STM1884 STM0321 STM2947 STM3709 STM3068 STM2141 STM1620 STM0368 STM4408 STM1291 STM0518 STM4184 STM4484 STM2317 STM3179 STM1480 STM4126 STM2338 STM2466 STM4467 STM2196 STM3240 STM0402 STM0608 STM2971 STM1826 STM1341   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.071426 (mmol/gDw/h)
  Minimum Production Rate : 0.163964 (mmol/gDw/h)

 Substrate: (mmol/gDw/h)
  EX_o2_e : 9.223548
  EX_glc__D_e : 5.000000
  EX_nh4_e : 0.787121
  EX_pi_e : 0.063341
  EX_k_e : 0.012685
  EX_so4_e : 0.008713
  EX_mg2_e : 0.000564
  EX_fe2_e : 0.000522
  EX_cl_e : 0.000338
  EX_ca2_e : 0.000338
  EX_cobalt2_e : 0.000226
  EX_cu2_e : 0.000226
  EX_mn2_e : 0.000226
  EX_mobd_e : 0.000226
  EX_zn2_e : 0.000226

Product: (mmol/gDw/h)
  EX_h2o_e : 12.082200
  EX_co2_e : 10.113118
  EX_dha_e : 4.928260
  EX_h_e : 0.773057
  EX_acald_e : 0.182224
  Auxiliary production reaction : 0.163964
  EX_glyclt_e : 0.003571
  DM_hmfurn_c : 0.000032

Visualization
  1. Download JSON file.
  2. Go to Escher site [3].

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.

Last updated: 27-Sep-2023
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