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 (100 of 113: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 38
  Gene deletion: STM1749 STM2463 STM2285 STM3526 STM0322 STM4567 STM4326 STM2947 STM3068 STM2141 STM1620 STM3542 STM4485 STM0491 STM0369 STM4408 STM1291 STM3069 STM4184 STM4484 STM2317 STM3179 STM1480 STM4126 STM2338 STM2466 STM3248 STM0519 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 : 0.144395 (mmol/gDw/h)
  Minimum Production Rate : 0.619023 (mmol/gDw/h)

 Substrate: (mmol/gDw/h)
  EX_o2_e : 12.998809
  EX_glc__D_e : 5.000000
  EX_nh4_e : 1.591256
  EX_pi_e : 0.128053
  EX_k_e : 0.025645
  EX_so4_e : 0.017614
  EX_mg2_e : 0.001140
  EX_fe2_e : 0.001058
  EX_ca2_e : 0.000684
  EX_cl_e : 0.000684
  EX_cobalt2_e : 0.000456
  EX_cu2_e : 0.000456
  EX_mn2_e : 0.000456
  EX_mobd_e : 0.000456
  EX_zn2_e : 0.000456

Product: (mmol/gDw/h)
  EX_h2o_e : 20.215654
  EX_co2_e : 16.234921
  EX_h_e : 1.850371
  Auxiliary production reaction : 0.619023
  EX_acald_e : 0.368386
  EX_glyclt_e : 0.007220
  DM_hmfurn_c : 0.000064

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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