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 (47 of 113: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 37
  Gene deletion: STM3646 STM0158 STM2927 STM1749 STM2463 STM2285 STM3526 STM4326 STM1511 STM1884 STM2952 STM2947 STM3709 STM3068 STM2141 STM1135 STM3597 STM4408 STM1291 STM4184 STM4484 STM2317 STM3179 STM4569 STM1480 STM4126 STM2338 STM2466 STM0977 STM1124 STM4467 STM2196 STM3240 STM0402 STM0608 STM2971 STM1826   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.071974 (mmol/gDw/h)
  Minimum Production Rate : 0.162793 (mmol/gDw/h)

Substrate: (mmol/gDw/h)
  EX_o2_e : 9.225960
  EX_glc__D_e : 5.000000
  EX_nh4_e : 0.793153
  EX_pi_e : 0.063826
  EX_k_e : 0.012783
  EX_so4_e : 0.008779
  EX_mg2_e : 0.000568
  EX_fe2_e : 0.000526
  EX_ca2_e : 0.000341
  EX_cl_e : 0.000341
  EX_cobalt2_e : 0.000227
  EX_cu2_e : 0.000227
  EX_mn2_e : 0.000227
  EX_mobd_e : 0.000227
  EX_zn2_e : 0.000227

Product: (mmol/gDw/h)
  EX_h2o_e : 12.096176
  EX_co2_e : 10.112005
  EX_dha_e : 4.927710
  EX_h_e : 0.772954
  EX_acald_e : 0.183620
  Auxiliary production reaction : 0.162793
  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.

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Last updated: 27-Sep-2023
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