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 : pa180_c
List of minimal gene deletion strategies (Download)

Gene deletion strategy (109 of 113: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 37
  Gene deletion: STM3646 STM1749 STM2463 STM2285 STM3526 STM4326 STM1511 STM1885 STM2952 STM2947 STM1135 STM4183 STM0491 STM0974 STM1326 STM4062 STM4408 STM1291 STM4484 STM0542 STM2317 STM3179 STM4569 STM1480 STM4126 STM0977 STM1124 STM4467 STM2196 STM3240 STM2051 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 : 0.064996 (mmol/gDw/h)
  Minimum Production Rate : 0.048239 (mmol/gDw/h)

Substrate: (mmol/gDw/h)
  EX_o2_e : 9.480188
  EX_glc__D_e : 5.000000
  EX_nh4_e : 0.716254
  EX_pi_e : 0.105878
  EX_k_e : 0.011543
  EX_so4_e : 0.007928
  EX_mg2_e : 0.000513
  EX_fe2_e : 0.000476
  EX_ca2_e : 0.000308
  EX_cl_e : 0.000308
  EX_cobalt2_e : 0.000205
  EX_cu2_e : 0.000205
  EX_mn2_e : 0.000205
  EX_mobd_e : 0.000205
  EX_zn2_e : 0.000205

Product: (mmol/gDw/h)
  EX_h2o_e : 12.255001
  EX_co2_e : 10.366722
  EX_dha_e : 4.934719
  EX_h_e : 0.551003
  EX_acald_e : 0.216803
  Auxiliary production reaction : 0.048239
  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.

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Last updated: 27-Sep-2023
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