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Table 3 Inconsistent gene essentiality predictions identified in refinement steps 2 and 3 and corresponding corrections and interpretations

From: Iterative reconstruction of a global metabolic model of Acinetobacter baylyi ADP1 using high-throughput growth phenotype and gene essentiality data

CORRECTION

  

56

NO CORRECTION

  

68

BIOMASS

  

10

Validated explanation

  

6

biomass precursor not essential

9

experimental error

1

   ACIAD0076 (rmlB)

D

step 2

 

   ACIAD0108 (lldD)

D

step 3

 

   ACIAD0078 (rmlD)

D

step 2

 

known gap in the understanding of pathway

4

   ACIAD0079 (rmlA)

D

step 2

 

   ACIAD0856 (bioA)

E

step 2

 

   ACIAD0080 (rmlC)

D

step 2

 

   ACIAD0857 (bioF)

E

step 2

 

   ACIAD0086 (epsM)

D

step 2

 

   ACIAD0859 (bioD)

E

step 2

 

   ACIAD0099 (galU)

D

step 2

 

   ACIAD2045 (bioB)

E

step 2

 

   ACIAD0101 (pgi)

D

step 2

 

unmodeled auxotrophy

1

   ACIAD0104 (manB)

D

step 2

 

   ACIAD3523 (metE)

E

step 2

 

   ACIAD2429 (cyoE)

D

step 2

 

Hypothetical explanation

32

missing essential biomass precursor

1

   ACIAD0178 (atpI)

E

step 2

 

   ACIAD1374 (ispU)

E

step 2

 

   ACIAD0180 (atpB)

E

step 2

 

GPR

34

   ACIAD0182 (atpE)

E

step 2

 

activity simultaneously requiring all genes

3

   ACIAD0183 (atpF)

E

step 2

 

   ACIAD0661 (hisG)

E

step 2

 

   ACIAD0184 (atpH)

E

step 2

 

   ACIAD1257 (hisZ)

E

step 2

 

   ACIAD0185 (atpA)

E

step 2

 

   ACIAD3103 (ilvH)

E

step 2

 

   ACIAD0186 (atpG)

E

step 2

 

gene associated to another essential reaction

1

   ACIAD0187 (atpD)

E

step 2

 

   ACIAD2606

E

step 2

 

   ACIAD0188 (atpC)

E

step 2

 

isozyme not functional

22

   ACIAD0556 (ndk)

D

step 2

 

   ACIAD0151 (guaA)

E

step 2

 

   ACIAD0650 (argJ)

E

step 2

 

   ACIAD0249 (ribC)

E

step 2

 

   ACIAD1150 (pyrC)

E

step 2

 

   ACIAD0871 (fabG)

E

step 2

 

   ACIAD1346 (sodB)

E

step 2

 

   ACIAD1069 (lysS)

E

step 2

 

   ACIAD1358 (rpiA)

E

step 2

 

   ACIAD1255 (epd)

E

step 2

 

   ACIAD2282 (sahH)

D

step 2

 

   ACIAD1323 (purF)

E

step 2

 

   ACIAD2314 (metZ)

E

step 2

 

   ACIAD1375 (cdsA)

E

step 2

 

   ACIAD2458 (glnA)

E

step 2

 

   ACIAD1736 (accC)

E

step 2

 

   ACIAD2842 (pckG)

E

step 2

 

   ACIAD1737 (accB)

E

step 2

 

   ACIAD2847 (folD)

E

step 2

 

   ACIAD1925 (fda)

E

step 2

 

   ACIAD3155 (mdh)

E

step 2

 

   ACIAD2227 (dctA)

E

step 2

 

   ACIAD3349 (gltD)

E

step 2

 

   ACIAD2565 (gap)

E

step 2

 

   ACIAD3350 (gltB)

E

step 2

 

   ACIAD2666

E

step 2

 

   ACIAD3470 (msuE)

E

step 2

 

   ACIAD2907 (prs)

E

step 2

 

   ACIAD3506 (aceF)

E

step 2

 

   ACIAD3062 (folK)

E

step 2

 

   ACIAD0101 (pgi)

E

step 3

 

   ACIAD3249 (ribA)

E

step 2

 

   ACIAD0546

E

step 3

 

   ACIAD3365 (murE)

E

step 2

 

   ACIAD0556 (ndk)

D

step 3

 

   ACIAD3371 (gltX)

E

step 2

 

   ACIAD1021

D

step 3

 

   ACIAD1710 (pcaC)

E

step 3

 

   ACIAD1707 (pcaB)

E

step 3

 

   ACIAD2018 (ald1)

E

step 3

 

   ACIAD1711 (pcaH)

E

step 3

 

   ACIAD2088 (aspQ)

E

step 3

 

   ACIAD1712 (pcaG)

E

step 3

 

   ACIAD2983 (gcd)

E

step 3

 

   ACIAD1744 (aspA)

E

step 3

 

presence of an alternate enzyme

6

No precise interpretation

30

   ACIAD1231 (argD)

D

step 2

 

   ACIAD0072 (ugd)

E

step 2

 

   ACIAD1642 (uppP)

D

step 2

 

   ACIAD0173 (rhtB)

E

step 2

 

   ACIAD2968 (ispA)

D

step 2

 

   ACIAD0382 (ubiB)

D

step 2

 

   ACIAD1020 (acoL)

D

step 3

 

   ACIAD0505 (purU1)

E

step 2

 

   ACIAD1715 (quiX)

D

step 3

 

   ACIAD1482 (kdsD)

D

step 2

 

   ACIAD2984

D

step 3

 

   ACIAD1483 (kdsC)

D

step 2

 

spontaneously occurring reaction

1

   ACIAD2283 (metF)

D

step 2

 

   ACIAD2819

D

step 3

 

   ACIAD2290 (cydA)

E

step 2

 

wrong complex subunit

1

   ACIAD2525

E

step 2

 

   ACIAD0799

D

step 2

 

   ACIAD2667 (pdxB)

D

step 2

 

NETWORK

12

   ACIAD2788

E

step 2

 

false alternate pathway in the model

7

   ACIAD2880 (sdhA)

D

step 2

 

   ACIAD0239 (ppa)

E

step 2

 

   ACIAD2911 (panD)

D

step 2

 

   ACIAD0547 (proA)

E

step 2

 

   ACIAD3503 (guaB)

E

step 2

 

   ACIAD1105 (adk)

E

step 2

 

   ACIAD3510 (lpxC)

D

step 2

 

   ACIAD1920 (glnS)

E

step 2

 

   ACIAD0086 (epsM)

E

step 3

 

   ACIAD2560 (proB)

E

step 2

 

   ACIAD0335 (fadB)

E

step 3

 

   ACIAD3032 (proC)

E

step 2

 

   ACIAD0382 (ubiB)

D

step 3

 

   ACIAD0901 (dut)

E

step 2

 

   ACIAD0922

E

step 3

 

missing alternate pathway in the model

5

   ACIAD2070 (metI)

E

step 3

 

   ACIAD0106 (lldP)

D

step 2

 

   ACIAD2282 (sahH)

D

step 3

 

   ACIAD0451 (katA)

D

step 2

 

   ACIAD2283 (metF)

D

step 3

 

   ACIAD0930 (glpK)

D

step 2

 

   ACIAD2667 (pdxB)

D

step 3

 

   ACIAD1045 (metH)

D

step 2

 

   ACIAD2755

E

step 3

 

   ACIAD0106 (lldP)

D

step 3

 

   ACIAD2875 (sucB)

E

step 3

 
    

   ACIAD2876 (sucA)

E

step 3

 
    

   ACIAD2880 (sdhA)

D

step 3

 
    

   ACIAD2911 (panD)

E

step 3

 
    

   ACIAD3071 (cysM)

E

step 3

 
    

   ACIAD3549 (gshA)

E

step 3

 
  1. Inconsistencies identified during the refinement steps using mutant library essentialities (step 2) and mutant growth phenotypes on 8 media (step 3). Inconsistencies leading to corrections (left column) are listed according to the model component that was corrected: GPR, NETWORK, and BIOMASS. Inconsistencies with no correction (right column) are listed according to the level of interpretation that could be drawn. Numbers provide the count of inconsistencies pertaining to each correction or interpretation category. For each inconsistency, E or D indicates the experimental phenotype of the mutant: E: gene is essential (on at least one medium for step 3), D gene is dispensable (on all media for step 3).
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BMC Systems Biology

ISSN: 1752-0509

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