MetNetComp Database [1] / Minimal gene deletions

Minimal gene deletions for simulation-based growth-coupled production. You can also see maximal gene deletions.

Model : iML1515 [2].
Target metabolite : ncam_c
List of minimal gene deletion strategies (Download)

Gene deletion strategy (115 of 116: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 43
  Gene deletion: b4467 b1478 b0474 b2518 b1241 b0351 b3831 b0910 b2221 b4152 b0871 b2297 b2458 b2925 b2097 b3617 b0030 b3844 b1004 b3713 b1109 b0046 b3236 b1612 b1611 b4122 b0651 b2162 b2690 b2210 b0614 b3945 b1602 b4138 b4123 b0621 b2913 b1380 b1695 b1206 b0606 b2285 b1009   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.459774 (mmol/gDw/h)
  Minimum Production Rate : 0.242827 (mmol/gDw/h)

 Substrate: (mmol/gDw/h)
  EX_fe2_e : 1000.000000
  EX_h_e : 990.959193
  EX_o2_e : 281.069331
  EX_glc__D_e : 10.000000
  EX_nh4_e : 5.617619
  EX_pi_e : 0.443501
  EX_so4_e : 0.115780
  EX_k_e : 0.089745
  EX_mg2_e : 0.003989
  EX_ca2_e : 0.002393
  EX_cl_e : 0.002393
  EX_cu2_e : 0.000326
  EX_mn2_e : 0.000318
  EX_zn2_e : 0.000157
  EX_ni2_e : 0.000149
  EX_cobalt2_e : 0.000011

Product: (mmol/gDw/h)
  EX_fe3_e : 999.992616
  EX_h2o_e : 546.597885
  EX_co2_e : 31.025058
  EX_succ_e : 1.562085
  EX_ac_e : 1.032567
  Auxiliary production reaction : 0.242827
  EX_ura_e : 0.083221
  DM_5drib_c : 0.000103
  DM_4crsol_c : 0.000103

Visualization
  1. Download JSON file.
  2. Go to Escher site [3].
  3. Select "Data > Load reaction data" and apply the downloaded file.

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: 21-Sep-2023
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