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tca-model.json
250 lines · skills/13c-metabolic-flux/assets/tca-model.json at 5f2bc03
1{
2 "schema_version": 1,
3 "name": "Published EMU TCA demonstration",
4 "flux_unit": "relative units; citrate synthase v1 fixed to 100",
5 "provenance": "Carbon network adapted from mfapy Example_0/1_toymodel_model.txt at a10433af16682386548b360297e2476152d46ede (MIT; see mfapy-license.txt). Numerical reference in Antoniewicz et al. 2007, Metabolic Engineering 9:68-86, DOI 10.1016/j.ymben.2006.09.001. Demonstration network, not a complete organism model.",
6 "metabolites": [
7 {
8 "id": "CO2ex",
9 "carbons": 1,
10 "boundary": "sink",
11 "symmetric": false
12 },
13 {
14 "id": "AcCoA",
15 "carbons": 2,
16 "boundary": "source",
17 "symmetric": false
18 },
19 {
20 "id": "OAC",
21 "carbons": 4,
22 "boundary": "internal",
23 "symmetric": false
24 },
25 {
26 "id": "Cit",
27 "carbons": 6,
28 "boundary": "internal",
29 "symmetric": false
30 },
31 {
32 "id": "AKG",
33 "carbons": 5,
34 "boundary": "internal",
35 "symmetric": false
36 },
37 {
38 "id": "Suc",
39 "carbons": 4,
40 "boundary": "internal",
41 "symmetric": true
42 },
43 {
44 "id": "Fum",
45 "carbons": 4,
46 "boundary": "internal",
47 "symmetric": true
48 },
49 {
50 "id": "Glu",
51 "carbons": 5,
52 "boundary": "internal",
53 "symmetric": false
54 },
55 {
56 "id": "Gluex",
57 "carbons": 5,
58 "boundary": "sink",
59 "symmetric": false
60 },
61 {
62 "id": "Asp",
63 "carbons": 4,
64 "boundary": "source",
65 "symmetric": false
66 }
67 ],
68 "reactions": [
69 {
70 "id": "v1",
71 "substrates": [
72 [
73 "AcCoA",
74 "AB"
75 ],
76 [
77 "OAC",
78 "CDEF"
79 ]
80 ],
81 "products": [
82 [
83 "Cit",
84 "FEDBAC"
85 ]
86 ],
87 "lower": 0.001,
88 "upper": 300,
89 "fixed": 100
90 },
91 {
92 "id": "v2",
93 "substrates": [
94 [
95 "Cit",
96 "ABCDEF"
97 ]
98 ],
99 "products": [
100 [
101 "AKG",
102 "ABCDE"
103 ],
104 [
105 "CO2ex",
106 "F"
107 ]
108 ],
109 "lower": 0.001,
110 "upper": 300
111 },
112 {
113 "id": "v3",
114 "substrates": [
115 [
116 "AKG",
117 "ABCDE"
118 ]
119 ],
120 "products": [
121 [
122 "Glu",
123 "ABCDE"
124 ]
125 ],
126 "lower": 0.001,
127 "upper": 300
128 },
129 {
130 "id": "v4",
131 "substrates": [
132 [
133 "AKG",
134 "ABCDE"
135 ]
136 ],
137 "products": [
138 [
139 "Suc",
140 "BCDE"
141 ],
142 [
143 "CO2ex",
144 "A"
145 ]
146 ],
147 "lower": 0.001,
148 "upper": 300
149 },
150 {
151 "id": "v5",
152 "substrates": [
153 [
154 "Suc",
155 "ABCD"
156 ]
157 ],
158 "products": [
159 [
160 "Fum",
161 "ABCD"
162 ]
163 ],
164 "lower": 0.001,
165 "upper": 300
166 },
167 {
168 "id": "v6",
169 "substrates": [
170 [
171 "Fum",
172 "ABCD"
173 ]
174 ],
175 "products": [
176 [
177 "OAC",
178 "ABCD"
179 ]
180 ],
181 "lower": 0.001,
182 "upper": 300
183 },
184 {
185 "id": "v7",
186 "substrates": [
187 [
188 "OAC",
189 "ABCD"
190 ]
191 ],
192 "products": [
193 [
194 "Fum",
195 "ABCD"
196 ]
197 ],
198 "lower": 0.001,
199 "upper": 300
200 },
201 {
202 "id": "v8",
203 "substrates": [
204 [
205 "Asp",
206 "ABCD"
207 ]
208 ],
209 "products": [
210 [
211 "OAC",
212 "ABCD"
213 ]
214 ],
215 "lower": 0.001,
216 "upper": 300
217 },
218 {
219 "id": "v9",
220 "substrates": [
221 [
222 "Glu",
223 "ABCDE"
224 ]
225 ],
226 "products": [
227 [
228 "Gluex",
229 "ABCDE"
230 ]
231 ],
232 "lower": 0.001,
233 "upper": 300
234 }
235 ],
236 "fragments": [
237 {
238 "id": "GluWhole",
239 "metabolite": "Glu",
240 "carbons": [
241 1,
242 2,
243 3,
244 4,
245 5
246 ],
247 "provenance": "All five glutamate carbons, matching the published EMU demonstration; not a derivatized GC-MS formula."
248 }
249 ]
250}