MetNetComp Database [1] / Core Genes

A set of core genes for simulation-based growth-coupled production. You can also see minimal gene deletions.

Model : iNJ661 [2].
Target metabolite : ump_c
Core genes for growth-coupled production (at least stoichioemetrically feasible)
  #Remaining genes : 248
  Remaining genes: Rv2281 Rv0545c Rv1559 Rv2051c Rv1201c Rv1822 Rv3396c Rv3784 Rv2156c Rv3266c Rv3465 Rv3068c Rv0489 Rv1739c Rv1437 Rv0946c Rv0728c Rv1511 Rv3696c Rv2392 Rv3846 Rv0391 Rv0500 Rv1079 Rv2539c Rv2552c Rv3356c Rv2335 Rv1338 Rv0858c Rv1202 Rv0808 Rv2386c Rv1286 Rv1692 Rv2476c Rv1285 Rv2958c Rv2962c Rv1493 Rv2465c Rv1492 Rv1408 Rv0570 Rv0855 Rv1981c Rv1878 Rv3051c Rv0046c Rv2701c Rv3048c Rv2220 Rv2860c Rv2222c Rv0137c Rv1389 Rv2124c Rv1392 Rv0070c Rv1512 Rv3582c Rv3581c Rv3436c Rv1617 Rv0389 Rv0408 Rv0436c Rv2243 Rv1436 Rv3042c Rv0884c Rv2381c Rv0993 Rv0437c Rv2383c Rv3227 Rv2380c Rv2382c Rv2379c Rv0619 Rv1017c Rv2378c Rv2384 Rv0618 Rv2611c Rv0620 Rv3255c Rv3808c Rv1603 Rv3264c Rv0788 Rv0803 Rv2934 Rv2932 Rv2210c Rv2935 Rv2883c Rv2933 Rv3302c Rv2931 Rv2928 Rv1551 Rv2122c Rv0780 Rv1606 Rv0334 Rv2157c Rv0809 Rv0772 Rv2152c Rv2155c Rv2610c Rv2153c Rv2163c Rv2158c Rv3838c Rv2957 Rv3754 Rv3809c Rv2702 Rv3634c Rv2941 Rv2136c Rv0382c Rv0482 Rv1653 Rv3818 Rv1018c Rv2321c Rv3628 Rv1315 Rv2322c Rv1612 Rv1613 Rv1385 Rv2503c Rv3308 Rv0295c Rv2504c Rv1656 Rv3265c Rv3490 Rv3372 Rv2006 Rv3913 Rv1699 Rv1438 Rv2754c Rv1449c Rv2075c Rv2949c Rv2920c Rv2445c Rv2540c Rv1885c Rv2612c Rv1011 Rv1383 Rv3001c Rv3710 Rv2988c Rv2121c Rv2987c Rv2995c Rv3565 Rv3709c Rv3393 Rv1380 Rv1843c Rv3410c Rv3411c Rv2246 Rv0957 Rv2201 Rv1611 Rv1601 Rv3708c Rv2245 Rv1605 Rv0098 Rv1001 Rv3800c Rv0644c Rv0470c Rv1609 Rv2192c Rv3624c Rv1023 Rv3772 Rv3379c Rv1294 Rv2870c Rv3423c Rv2981c Rv1599 Rv3398c Rv3248c Rv2538c Rv1652 Rv2537c Rv2182c Rv3273 Rv3792 Rv3793 Rv1381 Rv3795 Rv2139 Rv3794 Rv0357c Rv0777 Rv2763c Rv2753c Rv2773c Rv1555 Rv0189c Rv1553 Rv1086 Rv1554 Rv1552 Rv2178c Rv1099c Rv0363c Rv2940c Rv2881c Rv1662 Rv1663 Rv2726c Rv2524c Rv1293 Rv2947c Rv1350 Rv1484 Rv1323 Rv3801c Rv3340 Rv1529 Rv2334 Rv0733 Rv3313c Rv1655 Rv3002c Rv1820 Rv0409 Rv1654 Rv1302 Rv3280 Rv3281 Rv3815c   (List of alternative genes)
  Computed by: AddGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.006152 (mmol/gDw/h)
  Minimum Production Rate : 0.013268 (mmol/gDw/h)

 Substrate: (mmol/gDw/h)
  EX_glyc_e : 1.000000
  EX_nh4_e : 0.935864
  EX_o2_e : 0.454410
  EX_cit_e : 0.034598
  EX_pi_e : 0.020086
  EX_glu__L_e : 0.002758
  EX_so4_e : 0.000397

Product: (mmol/gDw/h)
  EX_h2o_e : 2.131709
  EX_h_e : 0.845828
  EX_ala__L_e : 0.806834
  EX_h2co3_e : 0.048433
  EX_phe__L_e : 0.030078
  EX_ppa_e : 0.014137
  Auxiliary production reaction : 0.013268
  EX_his__L_e : 0.011643
  EX_asp__L_e : 0.000030

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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