MetNetComp Database [1] / Core Genes A set of core genes for simulation-based growth-coupled production. You can also see minimal gene deletions.

Model : iPC815 [2].
Target metabolite : 3ophb_c
Core genes for growth-coupled production (at least stoichioemetrically feasible)
  #Remaining genes : 219
  Remaining genes: YPO1222 YPO0474 YPO2206 YPO2208 YPO2264 YPO3183 YPO4119 YPO0312 YPO1430 YPO0068 YPO3221 YPO2776 YPO2777 YPO1599 YPO1601 YPO2775 YPO2757 YPO2829 YPO3384 YPO3924 YPO4118 YPO1600 YPO1570 YPO3939 YPO3940 YPO2180 YPO1060 YPO0024 YPO3658 YPO3659 YPO3222 YPO2768 YPO3971 YPO2772 YPO2293 YPO2294 YPO1775 YPO0003 YPO0906 YPO0905 YPO0907 YPO0654 YPO1074 YPO2870 YPO3588 YPO3589 YPO2221 YPO2710 YPO1505 YPO2222 YPO1603 YPO0311 YPO1773 YPO3407 YPO1410 YPO0169 YPO2977 YPO3118 YPO3412 YPO1548 YPO1549 YPO1546 YPO4120 YPO4127 YPO4126 YPO4125 YPO4123 YPO4121 YPO4124 YPO4122 YPO1636 YPO3400 YPO0378 YPO1547 YPO1641 YPO1545 YPO1543 YPO0058 YPO2205 YPO0672 YPO3728 YPO3077 YPO3076 YPO3899 YPO3417 YPO2871 YPO0481 YPO0482 YPO1114 YPO0532 YPO1113 YPO0531 YPO0530 YPO0533 YPO2014 YPO1400 YPO2494 YPO3578 YPO2021 YPO2751 YPO2907 YPO0310 YPO2188 YPO1395 YPO0322 YPO1569 YPO1057 YPO1108 YPO3377 YPO3726 YPO1598 YPO3164 YPO3166 YPO3167 YPO3165 YPO1511 YPO0658 YPO2879 YPO3360 YPO3286 YPO0040 YPO3361 YPO1072 YPO1073 YPO3897 YPO0931 YPO0486 YPO2769 YPO0055 YPO0648 YPO1415 YPO1587 YPO0117 YPO3501 YPO1771 YPO0152 YPO3176 YPO0477 YPO0246 YPO3215 YPO2054 YPO3411 YPO3888 YPO1106 YPO1396 YPO3142 YPO1605 YPO2607 YPO4089 YPO3424 YPO1048 YPO3177 YPO0926 YPO0783 YPO0085 YPO2232 YPO2203 YPO2204 YPO1209 YPO1054 YPO3446 YPO3513 YPO1056 YPO2227 YPO0088 YPO0893 YPO0960 YPO0561 YPO0045 YPO1046 YPO0942 YPO3418 YPO3419 YPO3075 YPO4082 YPO1383 YPO1381 YPO3500 YPO3718 YPO2686 YPO3179 YPO2912 YPO1867 YPO1540 YPO1539 YPO1050 YPO2298 YPO3660 YPO4117 YPO3243 YPO3577 YPO4114 YPO4116 YPO1650 YPO4115 YPO1358 YPO3521 YPO3929 YPO0057 YPO2409 YPO0416 YPO3729 YPO2828 YPO0056 YPO4090 YPO1542 YPO3059 YPO2921 YPO1544 YPO2013 YPO1390 YPO0364 YPO3273 YPO1127 YPO2391 YPO3182 YPO3454 YPO0155 YPO0915   (List of alternative genes)
  Computed by: AddGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.011222 (mmol/gDw/h)
  Minimum Production Rate : 0.010243 (mmol/gDw/h)

Substrate: (mmol/gDw/h)
  EX_gly_e : 2.200000
  EX_h_e : 1.188359
  EX_o2_e : 0.829976
  EX_glc__D_e : 0.106690
  EX_pi_e : 0.009186
  EX_lys__L_e : 0.002806
  EX_phe__L_e : 0.002132
  EX_met__L_e : 0.001571
  EX_tyr__L_e : 0.001459
  EX_cys__L_e : 0.000819
  EX_cit_e : 0.000076

Product: (mmol/gDw/h)
  EX_nh4_e : 2.073785
  EX_co2_e : 1.901985
  EX_ac_e : 0.504419
  EX_h2o_e : 0.424568
  EX_akg_e : 0.188204
  EX_dha_e : 0.093350
  Auxiliary production reaction : 0.010243
  EX_ade_e : 0.000079
  EX_succ_e : 0.000076
  EX_glyc_e : 0.000059

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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