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 : pgp180_c
List of minimal gene deletion strategies (Download)

Gene deletion strategy (128 of 130: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 39
  Gene deletion: STM3646 STM1749 STM2463 STM2285 STM3526 STM1290 STM4326 STM1885 STM0517 STM2947 STM3068 STM2141 STM1135 STM2081 STM4183 STM0491 STM0368 STM4408 STM1291 STM4484 STM2317 STM3179 STM1480 STM4126 STM2338 STM2466 STM1124 STM4467 STM3802 STM2196 STM3240 STM0007 STM2473 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 : 0.065445 (mmol/gDw/h)
  Minimum Production Rate : 0.048095 (mmol/gDw/h)

 Substrate: (mmol/gDw/h)
  EX_o2_e : 9.041455
  EX_glc__D_e : 5.000000
  EX_nh4_e : 0.766170
  EX_pi_e : 0.154228
  EX_k_e : 0.011623
  EX_so4_e : 0.007983
  EX_mg2_e : 0.000517
  EX_fe2_e : 0.000478
  EX_ca2_e : 0.000310
  EX_cl_e : 0.000310
  EX_cu2_e : 0.000207
  EX_mn2_e : 0.000207
  EX_mobd_e : 0.000207
  EX_zn2_e : 0.000207
  EX_cobalt2_e : 0.000207

Product: (mmol/gDw/h)
  EX_h2o_e : 12.118743
  EX_co2_e : 9.945463
  EX_dha_e : 4.919281
  EX_h_e : 0.554953
  EX_acald_e : 0.166965
  Auxiliary production reaction : 0.048095
  EX_tyr__L_e : 0.044958
  EX_glyclt_e : 0.003272
  DM_hmfurn_c : 0.000029

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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