miniFROG Report_ALL.xlsx

	A	B	C	D	E	F	G	H	I	J	K	L	M
1	S.No	Publication	Organism	Model	Simulation constraints defined in publication	Type of simulation/Result	Tools used in publication	Results from publication	Line in FROG report	F/R/O/G	Predicted from FROG	Validation (Yes/No)	Remarks

2	1	https://doi.org/10.3389/fgene.2020.00116	Streptococccus Oralis	iCJ415	Biomass growth rate on Glycerol	Growth rates under a specified condition	COBRApy (FBA)	0	2	O	0	Yes
3					Cysteine auxotroph	Growth rates under a specified condition		0	2	O	0	Yes
4					Leucine auxotroph	Growth rates under a specified condition		1	2	O	16.5157	Yes
5					Growth in rich media	Number of essential genes under a specific condition		117		G	117	Yes	Count the Number of genes with zero growth
6					TPI KO in rich media	Single reaction deletion		58.69	92	R	58.65	Yes*
7					NADS1 KO in rich media	Single reaction deletion		100	244	R	100	Yes
8					TPI KO in glucose media	Single reaction deletion		0	92	R	0	Yes
9					NADS1 KO in glucose media	Single reaction deletion		100	244	R	0	No
10
11	2	https://doi.org/10.1016/j.mec.2019.e00101	Rhodosporidium toruloides	iRhtoC1108	Growth in M9 medium	Growth rates under a specified condition	COBRA (FBA)	0.19	2	O	0.1872	Yes
12					Growth using glucose as C-source	Growth rates under a specified condition		0.32	2	O	0.3191	Yes
13					Growth using xylose as C-source	Growth rates under a specified condition		0.009	2	O	0.0087	Yes
14					Arabitol production using xylose (uptake rate - 0.72 mmol/l/h)	Growth rates under a specified condition		0.451	2	O	0.4489	Yes*	The results observed exists within 5% of the reported value
15					Growth using Lysine as N-source	Growth rates under a specified condition		0	2	O	0	Yes
16					Gene essentiality - rt2682	Single gene deletion		Essential	459	G	0	Yes**	Growth rate of the respective KO strain was reported to represent the essentiality
17					Gene essentiality - rt6880	Single gene deletion		Non - essential	639	G	0.37672	Yes**
18					Gene essentiality - rt7828	Single gene deletion		Essential	112	G	0	Yes**
19
20	3	https://doi.org/10.1111/1462-2920.14843	Pseudomonas putida	iJN1462	Growth on ethanol as C-source	Growth rates under a specified condition	COBRApy (FBA)	1	2	O	0.2307	Yes**	Growth rate was reported to represent the growth phenotype
21					Growth on inosine as N-source	Growth rates under a specified condition		0	2	O	0	Yes**	Growth rate was reported to represent the growth phenotype
22					Growth on octanoate (uptake rate - 3.4 mmol/l/h)	Growth rates under a specified condition		0.2912	2	O	0.2912	Yes
23					Growth on glucose (uptake rate - 7.3 mmol/l/h)	Growth rates under a specified condition		0.71	2	O	0.714	Yes
24					Gene Essentiality - thrB (PP_0121)	Single gene deletion	COBRApy (MOMA)	Non-essential	829	G	0.6156	Yes**	Growth rate of the respective KO strain was reported to represent the essentiality
25					Gene Essentiality - bioC (PP_0365)	Single gene deletion		Non-essential	901	G	0	No
26					Gene Essentiality - argH (PP_0184)	Single gene deletion		Essential	266	G	0	Yes**
27
28	4	https://doi.org/10.1128/jb.00571-16	Methanococcus maripaludis	iMR539	Growth on hydrogen	Growth rates under a specified condition	COBRA (FBA)	0.09732	2	O	0.09732	Yes
29					Growth of double KO on hydrogen - ΔfdhA1ΔfdhA2	Growth rates under a specified condition		Non-lethal	2	O	0.09728	Yes**	Growth rate of the respective KO strain was reported to represent the essentiality
30					Growth on formate	Growth rates under a specified condition		0.0991	2	O	0.0991	Yes
31					Growth of double knockout on formate - ΔfdhA1ΔfdhA2	Growth rate of KO strain under a specified condition		Lethal	2	O	0	Yes**	Growth rate of the respective KO strain was reported to represent the essentiality
32					Gene essentiality on formate - hmd	Single gene deletion		Non-lethal	377	G	0.0991	Yes**
33					Gene essentiality on hydrogen - hmd (MMP0127)	Single gene deletion		Lethal	377	G	0.09732	No**
34					Maximum flux - ATPS	Flux variability under specific condition		24.573	536	F	24.573	Yes
35					Minimum flux - ATPS	Flux variability under specific condition		27.483	536	F	27.483	Yes
36					Maximum flux - ATPS	Flux variability under specific condition		27.846	536	F	27.846	Yes
37					Minimum flux - ATPS	Flux variability under specific condition		27.854	536	F	27.855	Yes
38
39	5	https://doi.org/10.3389/fmicb.2019.01283	Streptococcus pneumoniae	iDS372	Growth under anaerobic condition	Growth rates under a specified condition	OptFlux	0.784	2	O	0.7837	Yes
40					Growth under aerobic condition	Growth rates under a specified condition		1.051	2	O	1.0506	Yes
41					Growth on Glucose	Growth rates under a specified condition		0.85	2	O	0.8456	Yes
42					Growth on N-Acetyl D-Glucosamine	Growth rates under a specified condition		0.89	2	O	0.8917	Yes
43					Acetate production on Glucose	Metabolite production flux under a specified condition		0	384	F	0	Yes
44					Lactate production on Glucose	Metabolite production flux under a specified condition		66.7	383	F	67.28	No
45					Lactate production on N-Acetyl D-glucosamine	Metabolite production flux under a specified condition		70	383	F	70.58	Yes*
46					Acetate production on N-Acetyl D-glucosamine	Metabolite production flux under a specified condition		35.86	384	F	35.86	Yes
47					Gene Essentiality - spr1602	Single gene deletion		Non-essential	112	G	1.209	Yes**	Growth rate of the respective KO strain was reported to represent the essentiality
48					Gene Essentiality - spr0266	Single gene deletion		Essential	246	G	1.209	No**
49					Gene Essentiality - spr0438	Single gene deletion		Essential	238	G	0	Yes**
50					Number of essential genes	Single gene deletion		89		G	85	No*	Might vary because authors used optFlux to identify the essential gene
51
52	6	https://doi.org/10.1016/j.resmic.2015.12.005	Bacillus licheniformis	iXW1009	Growth on Galactose as C-source	Growth rates under a specified condition	COBRA (FBA)	1	2	O	3.9907	Yes
53					Growth on b-D-Allose as C-source	Growth rates under a specified condition		0	2	O	3.9907	No
54					Growth on D-Glucosamine as N-source	Growth rates under a specified condition		1	2	O	1.049	Yes
55					Growth of the knockout strain	Growth rate of KO strain under a specified condition		6.71	2	O	6.717	Yes
56					Growth in LB media	Number of essential genes under a specific condition		195		G	213	No*	The essential genes reported are the subset of the essential genes predicted. The discrepancy might be due to the lack of the in-silico media constraints
57					Growth in Glucose minimal media	Number of essential genes under a specific condition		235		G	266	No*
58					Gene Essentiality in LB - MUY_03190	Single gene deletion		Essential	861	G	0	Yes**	Growth rate of the respective KO strain was reported to represent the essentiality
59					Gene Essentiality in LB - MUY_03634	Single gene deletion		Non-Essential	171	G	22.876	Yes**
60					Gene Essentiality in minimal media - MUY_03190	Single gene deletion		Essential	861	G	0	Yes**
61					Gene Essentiality in minimal media - MUY_03634	Single gene deletion		Non-Essential	171	G	3.991	Yes**
62
63	7	https://doi.org/10.3389/fgene.2018.00121	Acinetobacter baumannii	iCN718	Growth on Succinate as C-source	Growth rates under a specified condition	COBRApy (FBA)	1	2	O	0.0836	Yes**	Growth rate of the respective KO strain was reported to represent the growth phenotype
64					Growth on Galactose as C-source	Growth rates under a specified condition		0	2	O	0	Yes**
65					Growth on Urea as N-source	Growth rates under a specified condition		1	2	O	0.3347	Yes**
66					Growth on L-Tyrosine as N-source	Growth rates under a specified condition		0	2	O	0	Yes**
67
68	8	doi:10.3390/microorganisms803043	Methylosinus trichosporium OB3b	iMsOB3b	Growth in copper-supplemented nitrate medium (Uptake rates from Table 1)	Growth rate	pFBA, COBRApy	0.123	2	O	0.122595	Yes
69					Growth on nitrate medium without copper (Uptake rates from Table 1)	Growth rate		0.109	2	O	0.109384	Yes
70					Flux distribution after knocking out the reaction 'FALDA'	Flux of EAOXRED		0.00009474820314	2	F	0.000095	Yes
71						Flux of IMPC		0.04138472779	3	F	0.041381	Yes
72						Flux of PANTS		0.00002692379063	5	F	0.000027	Yes
73
74	9	doi: 10.3390/ijms22042122	Escherichia coli Strain Nissle 1917	iDK1463	Aerobic growth, glucose uptake = -10	Growth	COBRApy	Growth	2	O	0.880331	Yes*	Growth rate value not reported
75					Essential genes for growth on glucose	Single gene deletions		195		G	196	No*	The names of the essential genes are not reported, only the number is given. Although the paper reports the total number of genes to be 1463, the attached xml file forms 1464 genes when read in MATLAB
76					Growth at anaerobic conditions on glucose	Growth rate		0.504	2	O	0.504277	Yes	At anaerobic condition, some reactions are activated
77					Growth at anaerobic conditions on N-acetylneuraminic acid	Growth rate		0.749	2	O	0.74929	Yes
78
79	10	doi: 10.1002/bit.25863	Pichia pastoris	ihGlycopastoris	Growth rate on glucose medium (Glucose uptake = 1)	Growth rate	SBML and RAVEN toolbox	0.0792	2	O	0.080241	Yes	The growth rate is deduced from Figure 2a
80					Theoretical yield of EPO	Maximum value of objective function		0.0061	2	O	0.006145	Yes	Supplementary data - S4
81					Theoretical yield of Alb	Maximum value of objective function		0.000845	2	O	0.000845	Yes	Supplementary data - S4
82
83	11	doi: 10.1007/s12010-020-03470-z	Thermotoga sp. Strain RQ7	RQ7_iJG408	Growth rate on MM1 (Table 2)	Growth rate	COBRApy	0.2	2	O	0.20017	Yes
84					No. of lethal genes on MM1	Single gene deletions		161		G	161	Yes
85					No. of lethal reactions on MM1	Single reaction deletions		273		R	273	Yes
86					Lethal gene - TRQ7_RS03135	Single gene deletions		lethal	25	G	0	Yes
87
88	12	doi: 10.1186/s12859-019-3134-5	Kluyveromyces marxianus	iSM996	Growth on glucose medium (glucose uptake = -1)	Growth	FBA	0.09065	2	O	0.09116	Yes	Growth rate value deduced from Figure 2b
89					Growth on melibiose			No growth	2	O	infeasible	Yes*	For all the cases where growth is not reported, the model simulation gives 'INFEASIBLE'
90					Growth on ethanol			Growth	2	O	0.0255	Yes*	Growth rate value not reported
91
92	13	doi: 10.1038/s41598-020-73253-3	Lachancea kluyveri	iPN730	Growth rate on glucose medium (Glucose uptake = -2.28, oxygen uptake = -6,2)	Growth rate	COBRA	0.2	2	O	0.2222	Yes*	The reported growth rate in paper could be the rounded-off value
93					Growth on melibiose			Growth	2	O	0	No
94					Growth on sucrose			Growth	2	O	0.295027	Yes
95					Growth on citrate			No growth	2	O	0	Yes
96					Essentiality of gene PCCGCIGL 06133	Single gene deletions		Essential for poor media	246	G	Growth rate = 0	Yes
97					Essentiality of gene PCCGCIGL 00527	Single gene deletions		Non-essential	133	G	Growth rate = 0.22	Yes
98
99	14	doi: 10.1101/2021.02.01.429138	Parageobacillus thermoglucosidasius NCIMB 11955	p-thermo	Biomass production in default medium	Growth rate	COBRA, pFBA	0.67	2	O	0.6655	Yes	Information from supplementary file 1.
100					Growth rate on mannose (aerobic)	Growth rate		between 0.35 and 0.4	2	O	0.361197	Yes	Growth rate value deduced from Figure 2b