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 (60 of 113: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 61
  Gene deletion: STM3010 STM0309 STM3646 STM1303 STM1463 STM0620 STM4290 STM3567 STM4398 STM3680 STM3513 STM3554 STM3970 STM2285 STM1522 STM4294 STM3091 STM4567 STM0680 STM1750 STM4568 STM1884 STM2952 STM0517 STM2283 STM3068 STM0704 STM2141 STM2977 STM0489 STM1135 STM4086 STM1680 STM3564 STM2081 STM0491 STM0370 STM3139 STM3062 STM0150 STM4184 STM4484 STM2317 STM2501 STM3179 STM3920 STM0659 STM4349 STM0221 STM3103 STM2297 STM1124 STM0588 STM2033 STM0007 STM2473 STM0644 STM2088 STM2774 STM2776 STM2864   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.091186 (mmol/gDw/h)
  Minimum Production Rate : 0.001182 (mmol/gDw/h)

Substrate: (mmol/gDw/h)
  EX_o2_e : 11.396438
  EX_glc__D_e : 5.000000
  EX_nh4_e : 1.067511
  EX_pi_e : 0.080864
  EX_k_e : 0.016195
  EX_so4_e : 0.011123
  EX_mg2_e : 0.000720
  EX_fe2_e : 0.000668
  EX_ca2_e : 0.000432
  EX_cl_e : 0.000432
  EX_cobalt2_e : 0.000288
  EX_cu2_e : 0.000288
  EX_mn2_e : 0.000288
  EX_mobd_e : 0.000288
  EX_zn2_e : 0.000288

Product: (mmol/gDw/h)
  EX_h2o_e : 14.198457
  EX_co2_e : 11.371444
  EX_dha_e : 4.887534
  EX_h_e : 0.898313
  EX_4abz_e : 0.062641
  EX_glyald_e : 0.000063
  DM_hmfurn_c : 0.000041

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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