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_c
List of minimal gene deletion strategies (Download)

Gene deletion strategy (87 of 105: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 35
  Gene deletion: STM1749 STM2463 STM4108 STM2285 STM3526 STM1290 STM4326 STM2947 STM3529 STM1620 STM0491 STM0368 STM4408 STM1291 STM4184 STM4484 STM2317 STM3179 STM1480 STM4126 STM2338 STM2466 STM3248 STM0519 STM1124 STM4467 STM3802 STM2196 STM3240 STM0402 STM0608 STM3708 STM2971 STM1826 STM1341   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.286418 (mmol/gDw/h)
  Minimum Production Rate : 0.011258 (mmol/gDw/h)

 Substrate: (mmol/gDw/h)
  EX_o2_e : 16.959432
  EX_glc__D_e : 5.000000
  EX_nh4_e : 3.156367
  EX_pi_e : 0.254002
  EX_k_e : 0.050868
  EX_so4_e : 0.034938
  EX_mg2_e : 0.002261
  EX_fe2_e : 0.002099
  EX_cl_e : 0.001357
  EX_ca2_e : 0.001357
  EX_cobalt2_e : 0.000905
  EX_cu2_e : 0.000905
  EX_mn2_e : 0.000905
  EX_mobd_e : 0.000905
  EX_zn2_e : 0.000905

Product: (mmol/gDw/h)
  EX_h2o_e : 25.191465
  EX_co2_e : 17.295403
  EX_h_e : 2.453724
  EX_acald_e : 0.730719
  EX_glyclt_e : 0.014321
  Auxiliary production reaction : 0.011258
  DM_hmfurn_c : 0.000128

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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