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Metabolic-regulatory network curation
Raw
gistfile1.txt
{
"metadata": {
"name": ""
},
"nbformat": 3,
"nbformat_minor": 0,
"worksheets": [
{
"cells": [
{
"cell_type": "heading",
"level": 1,
"metadata": {},
"source": [
"Scroll down for classified regulons from Fig. 6b"
]
},
{
"cell_type": "code",
"collapsed": false,
"input": [
"from pandas import DataFrame\n",
"from trnlib.omeORM import *\n",
"from IPython.core.display import HTML\n",
"\n",
"ome = Session()"
],
"language": "python",
"metadata": {},
"outputs": [],
"prompt_number": 91
},
{
"cell_type": "code",
"collapsed": false,
"input": [
"catabolism = {}\n",
"anabolism = {}\n",
"chemiosmosis = {}\n",
"unclassified = {}\n",
"global_regs = {}\n",
"double_regs = {}\n",
"tRNA_prophage = {}\n",
"\n",
"def flatten_to_genes(category):\n",
" genes = []\n",
" for x in category: \n",
" for y in category[x]:\n",
" try: \n",
" for z in category[x][y]: genes.append(z)\n",
" except:\n",
" genes.append(y)\n",
" return genes"
],
"language": "python",
"metadata": {},
"outputs": [],
"prompt_number": 90
},
{
"cell_type": "code",
"collapsed": false,
"input": [
"tfs = catabolism.keys()+anabolism.keys()+chemiosmosis.keys()\n",
"index = []\n",
"data = [[],[],[]]\n",
"for tf in set(tfs):\n",
" try: cat_genes = len(flatten_to_genes(catabolism[tf]))\n",
" except: cat_genes = 0\n",
" try: ana_genes = len(flatten_to_genes(anabolism[tf]))\n",
" except: ana_genes = 0\n",
" try: chem_genes = len(flatten_to_genes(chemiosmosis[tf]))\n",
" except: chem_genes = 0\n",
" index.append(tf)\n",
" data[0].append(cat_genes)\n",
" data[1].append(ana_genes)\n",
" data[2].append(chem_genes)\n",
" \n",
"df = DataFrame(index=index, data=array(data).T, columns=['Catabolic','Anabolic','Chemiosmotic'])"
],
"language": "python",
"metadata": {},
"outputs": [],
"prompt_number": 174
},
{
"cell_type": "code",
"collapsed": false,
"input": [
"HTML(df.sort('Catabolic').to_html())"
],
"language": "python",
"metadata": {},
"outputs": [
{
"html": [
"<table border=\"1\" class=\"dataframe\">\n",
" <thead>\n",
" <tr style=\"text-align: right;\">\n",
" <th></th>\n",
" <th>Catabolic</th>\n",
" <th>Anabolic</th>\n",
" <th>Chemiosmotic</th>\n",
" </tr>\n",
" </thead>\n",
" <tbody>\n",
" <tr>\n",
" <th>appY</th>\n",
" <td> 0</td>\n",
" <td> 0</td>\n",
" <td> 9</td>\n",
" </tr>\n",
" <tr>\n",
" <th>asnC</th>\n",
" <td> 0</td>\n",
" <td> 3</td>\n",
" <td> 0</td>\n",
" </tr>\n",
" <tr>\n",
" <th>fabR</th>\n",
" <td> 0</td>\n",
" <td> 2</td>\n",
" <td> 0</td>\n",
" </tr>\n",
" <tr>\n",
" <th>fhlA</th>\n",
" <td> 0</td>\n",
" <td> 0</td>\n",
" <td> 29</td>\n",
" </tr>\n",
" <tr>\n",
" <th>lysR</th>\n",
" <td> 0</td>\n",
" <td> 1</td>\n",
" <td> 0</td>\n",
" </tr>\n",
" <tr>\n",
" <th>argP</th>\n",
" <td> 0</td>\n",
" <td> 6</td>\n",
" <td> 1</td>\n",
" </tr>\n",
" <tr>\n",
" <th>birA</th>\n",
" <td> 0</td>\n",
" <td> 5</td>\n",
" <td> 0</td>\n",
" </tr>\n",
" <tr>\n",
" <th>metR</th>\n",
" <td> 0</td>\n",
" <td> 5</td>\n",
" <td> 1</td>\n",
" </tr>\n",
" <tr>\n",
" <th>narP</th>\n",
" <td> 0</td>\n",
" <td> 0</td>\n",
" <td> 47</td>\n",
" </tr>\n",
" <tr>\n",
" <th>putA</th>\n",
" <td> 1</td>\n",
" <td> 0</td>\n",
" <td> 0</td>\n",
" </tr>\n",
" <tr>\n",
" <th>nemR</th>\n",
" <td> 1</td>\n",
" <td> 0</td>\n",
" <td> 0</td>\n",
" </tr>\n",
" <tr>\n",
" <th>lldR</th>\n",
" <td> 1</td>\n",
" <td> 0</td>\n",
" <td> 1</td>\n",
" </tr>\n",
" <tr>\n",
" <th>dnaA</th>\n",
" <td> 1</td>\n",
" <td> 8</td>\n",
" <td> 0</td>\n",
" </tr>\n",
" <tr>\n",
" <th>betI</th>\n",
" <td> 1</td>\n",
" <td> 2</td>\n",
" <td> 0</td>\n",
" </tr>\n",
" <tr>\n",
" <th>trpR</th>\n",
" <td> 1</td>\n",
" <td> 13</td>\n",
" <td> 0</td>\n",
" </tr>\n",
" <tr>\n",
" <th>melR</th>\n",
" <td> 1</td>\n",
" <td> 0</td>\n",
" <td> 0</td>\n",
" </tr>\n",
" <tr>\n",
" <th>iscR</th>\n",
" <td> 1</td>\n",
" <td> 0</td>\n",
" <td> 24</td>\n",
" </tr>\n",
" <tr>\n",
" <th>dsdC</th>\n",
" <td> 2</td>\n",
" <td> 0</td>\n",
" <td> 0</td>\n",
" </tr>\n",
" <tr>\n",
" <th>kdgR</th>\n",
" <td> 2</td>\n",
" <td> 0</td>\n",
" <td> 0</td>\n",
" </tr>\n",
" <tr>\n",
" <th>murR</th>\n",
" <td> 2</td>\n",
" <td> 0</td>\n",
" <td> 0</td>\n",
" </tr>\n",
" <tr>\n",
" <th>mtlR</th>\n",
" <td> 2</td>\n",
" <td> 0</td>\n",
" <td> 0</td>\n",
" </tr>\n",
" <tr>\n",
" <th>dpiA</th>\n",
" <td> 2</td>\n",
" <td> 8</td>\n",
" <td> 1</td>\n",
" </tr>\n",
" <tr>\n",
" <th>xapR</th>\n",
" <td> 2</td>\n",
" <td> 0</td>\n",
" <td> 0</td>\n",
" </tr>\n",
" <tr>\n",
" <th>treR</th>\n",
" <td> 2</td>\n",
" <td> 0</td>\n",
" <td> 0</td>\n",
" </tr>\n",
" <tr>\n",
" <th>iclR</th>\n",
" <td> 3</td>\n",
" <td> 0</td>\n",
" <td> 0</td>\n",
" </tr>\n",
" <tr>\n",
" <th>tyrR</th>\n",
" <td> 3</td>\n",
" <td> 7</td>\n",
" <td> 0</td>\n",
" </tr>\n",
" <tr>\n",
" <th>metJ</th>\n",
" <td> 3</td>\n",
" <td> 9</td>\n",
" <td> 0</td>\n",
" </tr>\n",
" <tr>\n",
" <th>dhaR</th>\n",
" <td> 3</td>\n",
" <td> 0</td>\n",
" <td> 0</td>\n",
" </tr>\n",
" <tr>\n",
" <th>allS</th>\n",
" <td> 3</td>\n",
" <td> 0</td>\n",
" <td> 0</td>\n",
" </tr>\n",
" <tr>\n",
" <th>cynR</th>\n",
" <td> 3</td>\n",
" <td> 0</td>\n",
" <td> 0</td>\n",
" </tr>\n",
" <tr>\n",
" <th>dcuR</th>\n",
" <td> 3</td>\n",
" <td> 0</td>\n",
" <td> 4</td>\n",
" </tr>\n",
" <tr>\n",
" <th>rhaS</th>\n",
" <td> 4</td>\n",
" <td> 0</td>\n",
" <td> 0</td>\n",
" </tr>\n",
" <tr>\n",
" <th>prpR</th>\n",
" <td> 4</td>\n",
" <td> 0</td>\n",
" <td> 0</td>\n",
" </tr>\n",
" <tr>\n",
" <th>hcaR</th>\n",
" <td> 5</td>\n",
" <td> 0</td>\n",
" <td> 0</td>\n",
" </tr>\n",
" <tr>\n",
" <th>glpR</th>\n",
" <td> 5</td>\n",
" <td> 0</td>\n",
" <td> 4</td>\n",
" </tr>\n",
" <tr>\n",
" <th>gcvA</th>\n",
" <td> 5</td>\n",
" <td> 0</td>\n",
" <td> 0</td>\n",
" </tr>\n",
" <tr>\n",
" <th>rbsR</th>\n",
" <td> 5</td>\n",
" <td> 0</td>\n",
" <td> 0</td>\n",
" </tr>\n",
" <tr>\n",
" <th>uxuR</th>\n",
" <td> 5</td>\n",
" <td> 0</td>\n",
" <td> 0</td>\n",
" </tr>\n",
" <tr>\n",
" <th>xylR</th>\n",
" <td> 5</td>\n",
" <td> 0</td>\n",
" <td> 0</td>\n",
" </tr>\n",
" <tr>\n",
" <th>mhpR</th>\n",
" <td> 6</td>\n",
" <td> 0</td>\n",
" <td> 0</td>\n",
" </tr>\n",
" <tr>\n",
" <th>glcC</th>\n",
" <td> 6</td>\n",
" <td> 0</td>\n",
" <td> 0</td>\n",
" </tr>\n",
" <tr>\n",
" <th>idnR</th>\n",
" <td> 6</td>\n",
" <td> 0</td>\n",
" <td> 0</td>\n",
" </tr>\n",
" <tr>\n",
" <th>ulaR</th>\n",
" <td> 6</td>\n",
" <td> 0</td>\n",
" <td> 0</td>\n",
" </tr>\n",
" <tr>\n",
" <th>deoR</th>\n",
" <td> 6</td>\n",
" <td> 0</td>\n",
" <td> 0</td>\n",
" </tr>\n",
" <tr>\n",
" <th>nanR</th>\n",
" <td> 6</td>\n",
" <td> 0</td>\n",
" <td> 0</td>\n",
" </tr>\n",
" <tr>\n",
" <th>caiF</th>\n",
" <td> 7</td>\n",
" <td> 0</td>\n",
" <td> 4</td>\n",
" </tr>\n",
" <tr>\n",
" <th>nac</th>\n",
" <td> 7</td>\n",
" <td> 7</td>\n",
" <td> 0</td>\n",
" </tr>\n",
" <tr>\n",
" <th>narL</th>\n",
" <td> 8</td>\n",
" <td> 2</td>\n",
" <td> 101</td>\n",
" </tr>\n",
" <tr>\n",
" <th>allR</th>\n",
" <td> 8</td>\n",
" <td> 0</td>\n",
" <td> 0</td>\n",
" </tr>\n",
" <tr>\n",
" <th>cdaR</th>\n",
" <td> 9</td>\n",
" <td> 0</td>\n",
" <td> 0</td>\n",
" </tr>\n",
" <tr>\n",
" <th>araC</th>\n",
" <td> 9</td>\n",
" <td> 0</td>\n",
" <td> 0</td>\n",
" </tr>\n",
" <tr>\n",
" <th>cytR</th>\n",
" <td> 9</td>\n",
" <td> 2</td>\n",
" <td> 0</td>\n",
" </tr>\n",
" <tr>\n",
" <th>galR</th>\n",
" <td> 9</td>\n",
" <td> 0</td>\n",
" <td> 0</td>\n",
" </tr>\n",
" <tr>\n",
" <th>rutR</th>\n",
" <td> 9</td>\n",
" <td> 4</td>\n",
" <td> 2</td>\n",
" </tr>\n",
" <tr>\n",
" <th>galS</th>\n",
" <td> 9</td>\n",
" <td> 0</td>\n",
" <td> 0</td>\n",
" </tr>\n",
" <tr>\n",
" <th>fadR</th>\n",
" <td> 10</td>\n",
" <td> 1</td>\n",
" <td> 0</td>\n",
" </tr>\n",
" <tr>\n",
" <th>malT</th>\n",
" <td> 10</td>\n",
" <td> 0</td>\n",
" <td> 0</td>\n",
" </tr>\n",
" <tr>\n",
" <th>paaX</th>\n",
" <td> 11</td>\n",
" <td> 0</td>\n",
" <td> 0</td>\n",
" </tr>\n",
" <tr>\n",
" <th>gntR</th>\n",
" <td> 12</td>\n",
" <td> 0</td>\n",
" <td> 0</td>\n",
" </tr>\n",
" <tr>\n",
" <th>modE</th>\n",
" <td> 12</td>\n",
" <td> 0</td>\n",
" <td> 34</td>\n",
" </tr>\n",
" <tr>\n",
" <th>pdhR</th>\n",
" <td> 16</td>\n",
" <td> 21</td>\n",
" <td> 8</td>\n",
" </tr>\n",
" <tr>\n",
" <th>nagC</th>\n",
" <td> 20</td>\n",
" <td> 2</td>\n",
" <td> 3</td>\n",
" </tr>\n",
" <tr>\n",
" <th>purR</th>\n",
" <td> 20</td>\n",
" <td> 25</td>\n",
" <td> 1</td>\n",
" </tr>\n",
" <tr>\n",
" <th>cysB</th>\n",
" <td> 23</td>\n",
" <td> 0</td>\n",
" <td> 0</td>\n",
" </tr>\n",
" <tr>\n",
" <th>cra</th>\n",
" <td> 29</td>\n",
" <td> 8</td>\n",
" <td> 12</td>\n",
" </tr>\n",
" <tr>\n",
" <th>nsrR</th>\n",
" <td> 29</td>\n",
" <td> 11</td>\n",
" <td> 19</td>\n",
" </tr>\n",
" <tr>\n",
" <th>ntrC</th>\n",
" <td> 32</td>\n",
" <td> 1</td>\n",
" <td> 0</td>\n",
" </tr>\n",
" <tr>\n",
" <th>fnr</th>\n",
" <td> 33</td>\n",
" <td> 39</td>\n",
" <td> 81</td>\n",
" </tr>\n",
" <tr>\n",
" <th>argR</th>\n",
" <td> 41</td>\n",
" <td> 55</td>\n",
" <td> 11</td>\n",
" </tr>\n",
" <tr>\n",
" <th>lrp</th>\n",
" <td> 44</td>\n",
" <td> 40</td>\n",
" <td> 4</td>\n",
" </tr>\n",
" <tr>\n",
" <th>fur</th>\n",
" <td> 51</td>\n",
" <td> 10</td>\n",
" <td> 32</td>\n",
" </tr>\n",
" <tr>\n",
" <th>arcA</th>\n",
" <td> 98</td>\n",
" <td> 55</td>\n",
" <td> 67</td>\n",
" </tr>\n",
" <tr>\n",
" <th>crp</th>\n",
" <td> 253</td>\n",
" <td> 69</td>\n",
" <td> 42</td>\n",
" </tr>\n",
" </tbody>\n",
"</table>"
],
"metadata": {},
"output_type": "pyout",
"prompt_number": 175,
"text": [
"<IPython.core.display.HTML at 0x10bcc6c90>"
]
}
],
"prompt_number": 175
},
{
"cell_type": "heading",
"level": 1,
"metadata": {},
"source": [
"ArcA"
]
},
{
"cell_type": "code",
"collapsed": false,
"input": [
"catabolism['arcA'] = {\n",
" \"transport\": {\n",
" \"carbohydrate\": ['ptsG','mglA','mglB','mglC','kgtP','ugpB','ugpA','ugpE','ugpC','lldP','dcuA','dcuB'],\n",
" \"amino_acid\": ['potF','potG','potH','putP','oppA','oppB','oppC','oppD','oppF','hisJ','hisQ','hisM',\n",
" 'hisP','argT','gabP','sstT','dppA','dppB','dppC','dppD','dppF','cycA'],\n",
" \"nucleotides\": ['nupC'],\n",
" \"lipids\": [],\n",
" \"cofactors\": ['feoB']\n",
" },\n",
" \"recycling\": {\n",
" \"carbohydrate\": ['mhpC','mhpD','mhpE','mhpF','fsaA','paaK','manA','yeiG','suhB','uxaC','ugpQ','pldA'],\n",
" \"amino_acid\": ['caiA','clpA','clpS','putA','pepN','puuA','puuD','astC','astD','astE','ygjG','pepQ'],\n",
" \"lipids\": ['fadE','fadD','fadI','fadJ','fadH','fadA','fadB'],\n",
" \"nucleotides\": ['xseA']\n",
" },\n",
" \"glycolysis\": ['lpd','gapA'],\n",
" \"TCA\": ['acnB','gltA','sdhC','sdhA','sdhD','sdhB','sucA','sucB','sucC','sucD','icd',\n",
" 'aldA','fumA','glcB','glcD','glcE','glcF','glcG','mdh','fumB'],\n",
" \"accessory\": [],\n",
" \"regulators\": {\n",
" \"carbohydrate\": ['mhpR','ypdA','ypdB','glcC','aer'],\n",
" \"amino_acid\": ['puuR','gcvA','gcvB']\n",
" }\n",
" }\n",
"\n",
"anabolism['arcA'] = {\n",
" \"macromolecular_synthesis\": ['rpsT','xthA','rplY','ndk','ygjD','rpsU','dnaG','pnp','rpsO','rbfA','infB',\n",
" 'nusA','rpmA','rplU','nudE','mutM','rpmG','rpmB','recF','rpmH','rnpA'],\n",
" \"biosynthesis\": {\n",
" \"carbohydrate\": ['folE'],\n",
" \"nucleotides\": ['pncB','pntA','pntB','sthA'],\n",
" \"amino_acids\": ['thrA','thrB','thrC','carA','carB','leuD','gabD','gabT'],\n",
" \"lipids\": ['fabD','fabG','fabF',],\n",
" \"cofactors\": ['ribF','ispH','moaB','moaC','thiC','thiE','thiF','thiG','thiH','thiS']\n",
" },\n",
" \"accessory\": [],\n",
" \"regulators\": ['thrL','leuL','betI','bssR','infA','rcsB','cspA','rho']\n",
" }\n",
"\n",
"chemiosmosis['arcA'] = {\n",
" \"ETC\": {\n",
" \"dehydrogenases\": ['nuoA','nuoB','nuoC','nuoE','nuoF','nuoG','nuoH','nuoI','nuoJ','nuoK',\n",
" 'nuoL','nuoM','nuoN','hybA','hybB','hybC','hybD','hybE','hybF','hybG',\n",
" 'hybO','glpD','lldD','fdoG','fdoH','fdoI'],\n",
" \"oxidoreductases\": ['cyoA','cyoB','cyoC','cyoD','cyoE','cydA','cydB','dsbB','msrB','mqo',\n",
" 'lhgO','nrfA','nrfB','nrfC','nrfD','nrfF'],\n",
" \"accessory\": ['secG','glpE','glpG']\n",
" },\n",
" \"fermentation\": ['acs'],\n",
" \"ion_pumps\": ['kdpC','gsiB','gsiD','macA','cydD','cydC','cirA','ompC','mntH',\n",
" 'hemG','osmY'],\n",
" \"motility\": ['flhC','flhD'],\n",
" \"accessory\": ['tpx','yncE','yqcA'],\n",
" \"regulators\": ['glpR','gadX','gadW','micF','feoC']\n",
" }\n",
"\n",
"double_regs['arcA'] = ['rutR','argR','lldR']\n",
"\n",
"\n",
"\n",
"unclassified['arcA'] = ['ybfA','ybhK','ybiU','mcbA','ybjX','phoH','yceD','ynaJ','yncD','ydgC','rstA','rstB','yejG',\n",
" 'yfbM','ypdC','yfiF','csiD','yhgE','yhhJ','yhjE','yiaG','yieE','yigI','yigZ','yijD','yjcH',\n",
" 'yjiR','psrD','csrB']"
],
"language": "python",
"metadata": {},
"outputs": [],
"prompt_number": 96
},
{
"cell_type": "heading",
"level": 1,
"metadata": {},
"source": [
"Fnr"
]
},
{
"cell_type": "code",
"collapsed": false,
"input": [
"catabolism['fnr'] = {\n",
" \"transport\": {\n",
" \"carbohydrate\": ['ptsG','exuT'],\n",
" \"amino_acid\": ['aroP','metN','metI','metQ','potA','potB','potC','potD','tyrP'],\n",
" \"nucleotides\": ['uraA'],\n",
" \"lipids\": ['fadL']\n",
" },\n",
" \"recycling\": {\n",
" \"carbohydrate\": ['fsaA','arnA','mltA','envC'],\n",
" \"amino_acid\": ['pepT','yhbU','yhbV','ybiS','rnpA'],\n",
" \"lipids\": [],\n",
" \"nucleotides\": ['xseA']\n",
" },\n",
" \"glycolysis\": ['aceE','aceF','lpd','dhaK','dhaL','gapA','pykA','eno','gpmM'],\n",
" \"TCA\": [],\n",
" \"accessory\": [],\n",
" \"regulators\": {\n",
" \"carbohydrate\": ['caiF']\n",
" }\n",
" }\n",
"\n",
"anabolism['fnr'] = {\n",
" \"macromolecular_synthesis\": ['ddlA','pnp','truB','rbfA','recF','rpmH','nrdA','nrdB',\n",
" 'nrdD','upp','rplY','rpsU','nusA','infB','ung','nrdG',\n",
" 'groL'],\n",
" \"biosynthesis\": {\n",
" \"carbohydrate\": ['ybiS'],\n",
" \"nucleotides\": ['pyrD','guaA','guaB','purM','purN','purA','ravA','katG',\n",
" 'viaA'],\n",
" \"amino_acids\": ['thrB','thrC','argG','gltB','gltF','speA'],\n",
" \"lipids\": [],\n",
" \"cofactors\": []\n",
" },\n",
" \"accessory\": [],\n",
" \"regulators\": ['iraP','bssR','uspA','uspB','uspF','yfbV']\n",
" }\n",
"\n",
"chemiosmosis['fnr'] = {\n",
" \"ETC\": {\n",
" \"dehydrogenases\": ['nuoA','nuoB','nuoC','nuoE','nuoF','nuoG','nuoH','nuoI','nuoJ','nuoK',\n",
" 'nuoL','nuoM','nuoN','hybA','hybB','hybC','hybD','hybE','hybF','hybG',\n",
" 'hybO','fdnH','fdnI'],\n",
" \"oxidoreductases\": ['cydA','cydB','hcr','dmsA','dmsB','dmsC','narG','narH','narI','narJ',\n",
" 'frdA','frdB','frdC','frdD','nrfA','nrfB','nrfC','nrfD','nrfF','nirB',\n",
" 'nirD','nirC','ynfE','ynfF','ynfG','ynfH'],\n",
" \"accessory\": ['hcp','nikA','nikB','nikC','nikD','nikE','fhuF','dmsD',\n",
" 'ydhW','ydhY','secG','moaA','moaB','moaC','moaD','moaE']\n",
" },\n",
" \"fermentation\": ['pflB','focA','adhE','pta','ackA','yfiD'],\n",
" \"ion_pumps\": ['cydD','cydC','narK','pitA'],\n",
" \"motility\": [],\n",
" \"accessory\": ['msrB','ynjE','cysG'],\n",
" \"regulators\": ['narL','narX','nikR']\n",
" }\n",
"\n",
"double_regs['fnr'] = []\n",
"global_regs['fnr'] = ['pdhR','arcA']\n",
"\n",
"unclassified['fnr'] = ['uspF','ydcX','ydfZ','ynfK','ydjX','ydjY','ydjZ','ynjC','ynjD','ynjA','ynjB',\n",
" 'yhbT','yhbS','yfcZ','yeaD','yedE','yecH','yfcC','yggC','yghA','yghB','yqhA',\n",
" 'yqgC','yjeT','hsdS','hsdM','hsdR','yibN','csrB']\n",
"tRNA_prophage['fnr'] = ['yffL','metZ','metW','metV','yffS']"
],
"language": "python",
"metadata": {},
"outputs": [],
"prompt_number": 97
},
{
"cell_type": "heading",
"level": 1,
"metadata": {},
"source": [
"Fur"
]
},
{
"cell_type": "code",
"collapsed": false,
"input": [
"catabolism['fur'] = {\n",
" \"transport\": {\n",
" \"carbohydrate\": ['garP'],\n",
" \"amino_acid\": ['oppA','oppB','oppC','oppD','oppF'],\n",
" \"nucleotides\": [],\n",
" \"lipids\": [],\n",
" \"cofactors\": ['tonB','entS','fecA','fecB','fecC','fecD','fecE','fepA','fepC','fepD',\n",
" 'fepE','fepG','fepF','fepB','exbB','exbD','feoA','feoB','fhuA','fhuB',\n",
" 'fhuC','fhuD','fhuE','fhuF','fiu','mntH']\n",
" },\n",
" \"recycling\": {\n",
" \"carbohydrate\": ['garL','garR','garK'],\n",
" \"amino_acid\": ['gspO'],\n",
" \"lipids\": [],\n",
" \"nucleotides\": ['rnpB'],\n",
" \"cofactors\": ['fes']\n",
" },\n",
" \"glycolysis\": ['gpmA'],\n",
" \"TCA\": ['sdhA','sdhB','sdhC','sdhD','sucA','sucB','sucC','sucD','fumB'],\n",
" \"accessory\": [],\n",
" \"regulators\": {\n",
" \"carbohydrate\": [],\n",
" \"amino_acid\": [],\n",
" \"cofactors\": ['fecI','fecR','feoC',]\n",
" }\n",
" }\n",
"\n",
"anabolism['fur'] = {\n",
" \"macromolecular_synthesis\": ['ybdZ'],\n",
" \"biosynthesis\": {\n",
" \"carbohydrate\": [],\n",
" \"nucleotides\": ['nrdE','nrdF','nrdH','nrdI','pyrC','purF'],\n",
" \"amino_acids\": ['metH'],\n",
" \"lipids\": [],\n",
" \"cofactors\": []\n",
" },\n",
" \"accessory\": [],\n",
" \"regulators\": ['metJ','rpoS']\n",
" }\n",
"\n",
"chemiosmosis['fur'] = {\n",
" \"ETC\": {\n",
" \"dehydrogenases\": [],\n",
" \"oxidoreductases\": ['cyoA','cyoB','cyoC','cyoD','cyoE','yqjH'],\n",
" \"accessory\": []\n",
" },\n",
" \"fermentation\": [],\n",
" \"ion_pumps\": ['cirA','rcnA'],\n",
" \"motility\": ['flhC','flhD'],\n",
" \"accessory\": ['entA','entB','entC','entD','entH','entE','entF',\n",
" 'sufA','sufB','sufC','sufD', 'sufE','sufS','ftnA','hmp',\n",
" 'katE','katG','sodA','sodB','zinT'],\n",
" \"regulators\": ['rcnR','ryhB']\n",
" }\n",
"\n",
"double_regs['fur'] = ['purR']\n",
"\n",
"\n",
"\n",
"unclassified['fur'] = ['nohA','ydfN','ygaC','yhhY','yjjZ','ompF','tfaQ']\n",
"\n"
],
"language": "python",
"metadata": {},
"outputs": [],
"prompt_number": 98
},
{
"cell_type": "code",
"collapsed": false,
"input": [
"a = flatten_to_genes(catabolism['fur'])+flatten_to_genes(anabolism['fur'])+flatten_to_genes(chemiosmosis['fur'])+unclassified['fur']+double_regs['fur']\n",
"\n",
"\n",
"ome = Session()\n",
"ome.query(RegulatoryNetwork).filter_by(reg_gene='fur').filter(not_(RegulatoryNetwork.regd_gene.in_(a))).all()"
],
"language": "python",
"metadata": {},
"outputs": [
{
"metadata": {},
"output_type": "pyout",
"prompt_number": 99,
"text": [
"[RegulonDB fur --| fur]"
]
}
],
"prompt_number": 99
},
{
"cell_type": "heading",
"level": 1,
"metadata": {},
"source": [
"NtrC"
]
},
{
"cell_type": "code",
"collapsed": false,
"input": [
"catabolism['ntrC'] = {\n",
" \"transport\": {\n",
" \"carbohydrate\": [],\n",
" \"amino_acid\": ['argT','hisJ','hisQ','hisM','hisP','potF','potG','potH','potI',\n",
" 'ddpA','ddpB','ddpC','ddpD','ddpF','glnP','glnQ','glnH'],\n",
" \"nucleotides\": ['rutG'],\n",
" \"lipids\": [],\n",
" \"ions\": ['amtB'],\n",
" \"cofactors\": []\n",
" },\n",
" \"recycling\": {\n",
" \"carbohydrate\": [],\n",
" \"amino_acid\": ['astA','astB','astC','astD','astE','ddpX'],\n",
" \"lipids\": [],\n",
" \"nucleotides\": ['rutA','rutB','rutC','rutD','rutE','rutF'],\n",
" \"cofactors\": []\n",
" },\n",
" \"glycolysis\": [],\n",
" \"TCA\": [],\n",
" \"accessory\": [],\n",
" \"regulators\": {\n",
" \"carbohydrate\": [],\n",
" \"amino_acid\": [],\n",
" \"cofactors\": ['cbl']\n",
" }\n",
" }\n",
"\n",
"anabolism['ntrC'] = {\n",
" \"macromolecular_synthesis\": [],\n",
" \"biosynthesis\": {\n",
" \"carbohydrate\": [],\n",
" \"nucleotides\": [],\n",
" \"amino_acids\": ['glnA'],\n",
" \"lipids\": [],\n",
" \"cofactors\": []\n",
" },\n",
" \"accessory\": [],\n",
" \"regulators\": []\n",
" }\n",
"\n",
"chemiosmosis['ntrC'] = {\n",
" \"ETC\": {\n",
" \"dehydrogenases\": [],\n",
" \"oxidoreductases\": [],\n",
" \"accessory\": []\n",
" },\n",
" \"fermentation\": [],\n",
" \"ion_pumps\": [],\n",
" \"motility\": [],\n",
" \"accessory\": [],\n",
" \"regulators\": []\n",
" }\n",
"\n",
"double_regs['ntrC'] = ['glnK','glnL','nac']\n",
"\n",
"\n",
"\n",
"unclassified['ntrC'] = ['yeaG','yeaH','ygjG','yhdW','yhdX','yhdY','yhdZ']\n"
],
"language": "python",
"metadata": {},
"outputs": [],
"prompt_number": 100
},
{
"cell_type": "code",
"collapsed": false,
"input": [
"a = flatten_to_genes(catabolism['ntrC'])+flatten_to_genes(anabolism['ntrC'])+flatten_to_genes(chemiosmosis['ntrC'])+unclassified['ntrC']+double_regs['ntrC']\n",
"\n",
"\n",
"\n",
"ome.query(RegulatoryNetwork).filter_by(reg_gene='glnG').filter(not_(RegulatoryNetwork.regd_gene.in_(a))).all()"
],
"language": "python",
"metadata": {},
"outputs": [
{
"metadata": {},
"output_type": "pyout",
"prompt_number": 101,
"text": [
"[RegulonDB glnG --? glnG]"
]
}
],
"prompt_number": 101
},
{
"cell_type": "heading",
"level": 1,
"metadata": {},
"source": [
"Nac"
]
},
{
"cell_type": "code",
"collapsed": false,
"input": [
"catabolism['nac'] = {\n",
" \"transport\": {\n",
" \"carbohydrate\": [],\n",
" \"amino_acid\": ['gabP'],\n",
" \"lipids\": [],\n",
" \"nucleotides\": ['codB','nupC'],\n",
" \"cofactors\": []\n",
" },\n",
" \"recycling\": {\n",
" \"carbohydrate\": ['gabD'],\n",
" \"amino_acid\": ['gabT'],\n",
" \"lipids\": [],\n",
" \"nucleotides\": ['codA'],\n",
" \"cofactors\": []\n",
" },\n",
" \"glycolysis\": [],\n",
" \"TCA\": [],\n",
" \"accessory\": [],\n",
" \"regulators\": {\n",
" \"carbohydrate\": ['asnC'],\n",
" \"amino_acid\": [],\n",
" \"cofactors\": []\n",
" }\n",
" }\n",
"\n",
"anabolism['nac'] = {\n",
" \"macromolecular_synthesis\": ['mnmG'],\n",
" \"biosynthesis\": {\n",
" \"carbohydrate\": ['mioC'],\n",
" \"nucleotides\": [],\n",
" \"amino_acids\": ['serA','gdhA','gltB','gltD','gltF'],\n",
" \"lipids\": [],\n",
" \"cofactors\": []\n",
" },\n",
" \"accessory\": [],\n",
" \"regulators\": []\n",
" }\n",
"\n",
"chemiosmosis['nac'] = {\n",
" \"ETC\": {\n",
" \"dehydrogenases\": [],\n",
" \"oxidoreductases\": [],\n",
" \"accessory\": []\n",
" },\n",
" \"fermentation\": [],\n",
" \"ion_pumps\": [],\n",
" \"motility\": [],\n",
" \"accessory\": [],\n",
" \"regulators\": []\n",
" }\n",
"\n",
"double_regs['nac'] = []\n",
"\n",
"\n",
"\n",
"unclassified['nac'] = []\n"
],
"language": "python",
"metadata": {},
"outputs": [],
"prompt_number": 102
},
{
"cell_type": "code",
"collapsed": false,
"input": [
"a = flatten_to_genes(catabolism['nac'])+flatten_to_genes(anabolism['nac'])+flatten_to_genes(chemiosmosis['nac'])+unclassified['nac']+double_regs['nac']\n",
"\n",
"\n",
"\n",
"ome.query(RegulatoryNetwork).filter_by(reg_gene='nac').filter(not_(RegulatoryNetwork.regd_gene.in_(a))).all()"
],
"language": "python",
"metadata": {},
"outputs": [
{
"metadata": {},
"output_type": "pyout",
"prompt_number": 103,
"text": [
"[RegulonDB nac --| nac]"
]
}
],
"prompt_number": 103
},
{
"cell_type": "heading",
"level": 1,
"metadata": {},
"source": [
"ModE"
]
},
{
"cell_type": "code",
"collapsed": false,
"input": [
"catabolism['modE'] = {\n",
" \"transport\": {\n",
" \"carbohydrate\": [],\n",
" \"amino_acid\": ['oppA','oppB','oppC','oppD','oppF'],\n",
" \"lipids\": [],\n",
" \"nucleotides\": [],\n",
" \"cofactors\": ['modA','modB','modC']\n",
" },\n",
" \"recycling\": {\n",
" \"carbohydrate\": [],\n",
" \"amino_acid\": [],\n",
" \"lipids\": [],\n",
" \"nucleotides\": ['deoA','deoB','deoC','deoD'],\n",
" \"cofactors\": []\n",
" },\n",
" \"glycolysis\": [],\n",
" \"TCA\": [],\n",
" \"accessory\": [],\n",
" \"regulators\": {\n",
" \"carbohydrate\": [],\n",
" \"amino_acid\": [],\n",
" \"cofactors\": []\n",
" }\n",
" }\n",
"\n",
"anabolism['modE'] = {\n",
" \"macromolecular_synthesis\": [],\n",
" \"biosynthesis\": {\n",
" \"carbohydrate\": [],\n",
" \"nucleotides\": [],\n",
" \"amino_acids\": [],\n",
" \"lipids\": [],\n",
" \"cofactors\": []\n",
" },\n",
" \"accessory\": [],\n",
" \"regulators\": []\n",
" }\n",
"\n",
"chemiosmosis['modE'] = {\n",
" \"ETC\": {\n",
" \"dehydrogenases\": ['hycB','hycC','hycD','hycE','hycF','hycG'],\n",
" \"oxidoreductases\": ['napA','napB','napC','napD','napF','napG','napH','dmsA','dmsB',\n",
" 'dmsC'],\n",
" \"accessory\": ['ccmA','ccmB','ccmC','ccmD','ccmE','ccmF','ccmG','ccmH',\n",
" 'moaA','moaB','moaC','moaD','moaE','hycH','hycI']\n",
" },\n",
" \"fermentation\": [],\n",
" \"ion_pumps\": [],\n",
" \"motility\": [],\n",
" \"accessory\": [],\n",
" \"regulators\": ['hycA','narL','narX']\n",
" }\n",
"\n",
"double_regs['modE'] = []\n",
"\n",
"\n",
"\n",
"unclassified['modE'] = []\n"
],
"language": "python",
"metadata": {},
"outputs": [],
"prompt_number": 104
},
{
"cell_type": "code",
"collapsed": false,
"input": [
"a = flatten_to_genes(catabolism['modE'])+flatten_to_genes(anabolism['modE'])+flatten_to_genes(chemiosmosis['modE'])+unclassified['modE']+double_regs['modE']\n",
"\n",
"\n",
"\n",
"ome.query(RegulatoryNetwork).filter_by(reg_gene='modE').filter(not_(RegulatoryNetwork.regd_gene.in_(a))).all()"
],
"language": "python",
"metadata": {},
"outputs": [
{
"metadata": {},
"output_type": "pyout",
"prompt_number": 105,
"text": [
"[]"
]
}
],
"prompt_number": 105
},
{
"cell_type": "heading",
"level": 1,
"metadata": {},
"source": [
"IscR"
]
},
{
"cell_type": "code",
"collapsed": false,
"input": [
"catabolism['iscR'] = {\n",
" \"transport\": {\n",
" \"carbohydrate\": [],\n",
" \"amino_acid\": [],\n",
" \"lipids\": [],\n",
" \"nucleotides\": [],\n",
" \"cofactors\": []\n",
" },\n",
" \"recycling\": {\n",
" \"carbohydrate\": [],\n",
" \"amino_acid\": [],\n",
" \"lipids\": [],\n",
" \"nucleotides\": ['rnlA'],\n",
" \"cofactors\": []\n",
" },\n",
" \"glycolysis\": [],\n",
" \"TCA\": [],\n",
" \"accessory\": [],\n",
" \"regulators\": {\n",
" \"carbohydrate\": [],\n",
" \"amino_acid\": [],\n",
" \"cofactors\": []\n",
" }\n",
" }\n",
"\n",
"anabolism['iscR'] = {\n",
" \"macromolecular_synthesis\": [],\n",
" \"biosynthesis\": {\n",
" \"carbohydrate\": [],\n",
" \"nucleotides\": [],\n",
" \"amino_acids\": [],\n",
" \"lipids\": [],\n",
" \"cofactors\": []\n",
" },\n",
" \"accessory\": [],\n",
" \"regulators\": []\n",
" }\n",
"\n",
"chemiosmosis['iscR'] = {\n",
" \"ETC\": {\n",
" \"dehydrogenases\": ['hyaA','hyaB','hyaC','hyaD','hyaE','hyaF'],\n",
" \"oxidoreductases\": ['napA','napB','napC','napD','napF','napG','napH'],\n",
" \"accessory\": ['erpA']\n",
" },\n",
" \"fermentation\": [],\n",
" \"ion_pumps\": [],\n",
" \"motility\": [],\n",
" \"accessory\": ['sufA','sufB','sufC','sufD', 'sufE','sufS','nfuA',\n",
" 'iscA','iscS','iscU'],\n",
" \"regulators\": []\n",
" }\n",
"\n",
"double_regs['iscR'] = []\n",
"\n",
"\n",
"\n",
"unclassified['iscR'] = ['ydiU']\n"
],
"language": "python",
"metadata": {},
"outputs": [],
"prompt_number": 106
},
{
"cell_type": "code",
"collapsed": false,
"input": [
"a = flatten_to_genes(catabolism['iscR'])+flatten_to_genes(anabolism['iscR'])+flatten_to_genes(chemiosmosis['iscR'])+unclassified['iscR']+double_regs['iscR']\n",
"\n",
"\n",
"ome.query(RegulatoryNetwork).filter_by(reg_gene='iscR').filter(not_(RegulatoryNetwork.regd_gene.in_(a))).all()"
],
"language": "python",
"metadata": {},
"outputs": [
{
"metadata": {},
"output_type": "pyout",
"prompt_number": 107,
"text": [
"[RegulonDB iscR --| iscR]"
]
}
],
"prompt_number": 107
},
{
"cell_type": "heading",
"level": 1,
"metadata": {},
"source": [
"Lrp"
]
},
{
"cell_type": "code",
"collapsed": false,
"input": [
"catabolism['lrp'] = {\n",
" \"transport\": {\n",
" \"carbohydrate\": [],\n",
" \"amino_acid\": ['brnQ','potF','potG','potH','artM','artQ','artI','artP','oppC','leuE','ygaW','sdaC',\n",
" 'yqeG','sstT','livF','livG','livM','livH','livK','dtpB','dppA','dppB','dppC','dppD','dppF',\n",
" 'gltP'\n",
" ],\n",
" \"nucleotides\": [],\n",
" \"lipids\": ['fadL']\n",
" },\n",
" \"recycling\": {\n",
" \"carbohydrate\": ['yqeF'],\n",
" \"amino_acid\": ['pepD','ompT','sdaA','sdaB','gcvP','gcvH','gcvT','tdhA','kbl'],\n",
" \"lipids\": [],\n",
" \"nucleotides\": ['upp']\n",
" },\n",
" \"glycolysis\": ['dhaK','dhaL','dhaM'],\n",
" \"TCA\": ['aceK'],\n",
" \"accessory\": ['eco'],\n",
" \"regulators\": {\n",
" \"carbohydrate\": ['araC']\n",
" }\n",
" }\n",
"\n",
"anabolism['lrp'] = {\n",
" \"macromolecular_synthesis\": ['lplA'],\n",
" \"biosynthesis\": {\n",
" \"carbohydrate\": ['folM','yhhK'],\n",
" \"nucleotides\": ['galU','purM','purN',],\n",
" \"amino_acids\": ['thrA','thrB','thrC','leuD','leuC','leuB','leuA','leuL','ilvI','ilvH','aroG',\n",
" 'dadX','yfbQ','serA','ansB','gltB','gltD','gltF','avtA','ilvL','ilvM','ilvE',\n",
" 'ilvA','lysU'],\n",
" \"lipids\": []\n",
" },\n",
" \"regulators\": ['ftsQ','ftsA','ftsZ','topA','uspE','lexA','yciT','stpA','fimA','fimC']\n",
" }\n",
"\n",
"chemiosmosis['lrp'] = {\n",
" \"ETC\": {\n",
" \"dehydrogenases\": ['dadA'],\n",
" \"oxidoreductases\": ['napC'],\n",
" \"accessory\": ['ccmE']\n",
" },\n",
" \"fermentation\": [],\n",
" \"ion_pumps\": [],\n",
" \"motility\": [],\n",
" \"regulators\": ['gadY']\n",
" }\n",
"\n",
"unclassified['lrp'] = ['ybgS','ybhP','ybhQ','ybiJ','ycgB','yciN','yfcC','yfcZ','yffR','csiE','yhjE','yjbJ','yjbQ','yjbR','ytfJ']"
],
"language": "python",
"metadata": {},
"outputs": [],
"prompt_number": 108
},
{
"cell_type": "heading",
"level": 1,
"metadata": {},
"source": [
"Crp"
]
},
{
"cell_type": "code",
"collapsed": false,
"input": [
"catabolism['crp'] = {\n",
" \"transport\": {\n",
" \"carbohydrate\": ['agaV','agp','araE','araF','araG','araH','ascF','bglG','chbA','chbB','chbC','dctA',\n",
" 'dcuA','dcuB','exuT','fucP','galP','gatA','gatB','gatC','gntU','idnT','lacY','lamB',\n",
" 'malK','malF','malG','malE','manX','manZ','manY','mglA','mglB','mglC','mtlA','murP',\n",
" 'nagE','nanT','nanC','ptsG','ptsH','ptsI','rbsA','rbsB','rbsC','rhaT','srlA','srlB',\n",
" 'srlE','treB','ugpA','ugpB','ugpC','ugpE','uhpT','uidB','ulaA','ulaB','ulaC','xylF',\n",
" 'xylG','xylH','yiaM','yiaN','yiaO','crr'],\n",
" \"amino_acid\": ['cirA','dsdX','gabP','lsrA','lsrB','lsrC','lsrD','melB','proP','sohB','tdcC','tnaB'],\n",
" \"nucleotides\": ['nupC','nupG','tsx'],\n",
" \"lipids\": ['fadL'],\n",
" \"cofactors\": ['modA','modB','modC']\n",
" },\n",
" \"recycling\": {\n",
" \"carbohydrate\": ['araB','araA','araD','ascB','bglB','bglF','caiA','caiB','caiC','caiD','caiD','caiE',\n",
" 'chbF','chbG','chbA','chbR','fucA','fucO','fucK','fucI','galE','galT','galK','galM','gatD',\n",
" 'gatZ','gatY','gutQ','hofM','hofN','hofO','hofP','idnD','idnK','paaA','idnO','kbaZ','lacA',\n",
" 'lacZ','lsrF','lsrG','lyxK','malS','melA','metK','mtlD','murQ','nagA','nagB','nanA','nanE',\n",
" 'nanK','nanM','paaB','paaC','paaD','paaF','paaG','paaH','paaI','paaJ','paaK','maoC','prpB',\n",
" 'prpC','prpD','prpE','rbsD','rbsK','rhaA','rhaB','sgbE','sgbh','sgbU','srlD','tam','treC',\n",
" 'ugpQ','uidA','uidC','ulaD','ulaE','ulaF','uxaA','uxaB','uxaC','uxuA','uxuB','xylA','xylB',\n",
" 'yiaK','yiaL'],\n",
" \"amino_acid\": ['cdd','dsdA','mhpC','mhpF','putP','speC','tdcB','tdcC','tdcD','tdcE','tdcF','tdcG','tnaA'],\n",
" \"lipids\": ['mpl'],\n",
" \"nucleotides\": ['cyaR','deoA','deoB','deoC','deoD','hpt','udp','xseA']\n",
" },\n",
" \"glycolysis\": ['aceE','aceF','fbaA','gapA','pgk'],\n",
" \"TCA\": ['aceB','aceA','aceK','acnA','acnB','aspA','fumA','fumB','mdh','sdhA','sdhB','sdhC','sdhD',\n",
" 'sucA','sucB','sucC','sucD'],\n",
" \"accessory\": ['aldA','aldB',],\n",
" \"regulators\": {\n",
" \"carbohydrate\": ['aer','araC','caiT','cstA','cyaA','dcuR','dgsA','feaR','galS','glcC','gutM',\n",
" 'idnR','malT','melR','mtlR','nagC','pdhR','prpR','rbsR','rhaR','rhaS','sfsA','srlR','uxuR',\n",
" 'xylR','yiaJ','caiF'],\n",
" \"nucleotides\": ['cytR'],\n",
" \"amino_acid\": ['tdcA','tnaC'] \n",
" }\n",
" }\n",
"\n",
"anabolism['crp'] = {\n",
" \"macromolecular_synthesis\": ['cpdB','dusB','metY','nrdA','nrdB','ppiA','rimP','rpoH','rpoS','rpsO','truB','pnp'],\n",
" \"biosynthesis\": {\n",
" \"carbohydrate\": ['glgA','glgC','glgP'],\n",
" \"nucleotides\": ['epd','guaA','guaB','nagD','pncB','yeiA','yeiT','ubiG'],\n",
" \"amino_acids\": ['gdhA','ansB','argG','aroA','dadX','gabD','gabT','glnA','ilvB','ilvN','mhpD','mhpE',\n",
" 'serA','serC'],\n",
" \"lipids\": ['fadD','fadH']\n",
" },\n",
" \"accessory\": ['entA','entB','entC','entD','entE','entH','fecA','fecB','fecC','fecD','fecE',\n",
" 'fepA','nfuA','zraR','zraS'],\n",
" \"regulators\": ['csgF','fur','glgS','glnG','glnL','grpE','gyrA','hupA','hupB','infB','ivbL','lsrR',\n",
" 'nusA','rbfA','spf']\n",
" }\n",
"\n",
"chemiosmosis['crp'] = {\n",
" \"ETC\": {\n",
" \"dehydrogenases\": ['gcd','dadA'],\n",
" \"oxidoreductases\": ['cyoA','cyoB','cyoC','cyoD','cyoE','fixA','fixB','fixC','fixX','lhgO','nirB',\n",
" 'nirD','nirC'],\n",
" \"accessory\": ['cysG','trxA']\n",
" },\n",
" \"fermentation\": ['acs','actP','focA','focB','hyfA','hyfB','hyfC','hyfD','hyfE','hyfG','hyfH'\n",
" 'hyfI','hyfJ','hyfR','pflB','yjcH'],\n",
" \"ion_pumps\": ['osmY'],\n",
" \"motility\": ['flhC','flhD'],\n",
" \"regulators\": ['gadX'],\n",
" \"pH\": ['gadA','gadB','gadC','gadE','sodA','sodB'],\n",
" }\n",
"\n",
"unclassified['crp'] = ['azuC','chpA','chpR','cdgD','csgE','csgG','csiD','csiE','dksA','envZ','fis','ybiL','hlyE','hofB','hofC',\n",
" 'marA','marB','marR','mdtE','mdtF','ompA','ompF','ompR','oxyR','ppdD','psiE','relA','sbmC','trg',\n",
" 'ychH','yhfA','ykgR','ynfK']"
],
"language": "python",
"metadata": {},
"outputs": [],
"prompt_number": 109
},
{
"cell_type": "heading",
"level": 1,
"metadata": {},
"source": [
"PurR"
]
},
{
"cell_type": "code",
"collapsed": false,
"input": [
"catabolism['purR'] = {\n",
" \"transport\": {\n",
" \"carbohydrate\": [],\n",
" \"amino_acid\": ['sdaC','gltS','gltP'],\n",
" \"nucleotides\": ['codB','tsx','uraA','xanP','yieG'],\n",
" \"lipids\": []\n",
" },\n",
" \"recycling\": {\n",
" \"carbohydrate\": ['glpQ','glpT'],\n",
" \"amino_acid\": ['sdaB','gcvP','gcvH','gcvT'],\n",
" \"lipids\": ['mltF'],\n",
" \"nucleotides\": ['upp','xseA','yieH','codA']\n",
" },\n",
" \"glycolysis\": [],\n",
" \"TCA\": [],\n",
" \"accessory\": [],\n",
" \"regulators\": {\n",
" \"carbohydrate\": ['malT']\n",
" }\n",
" }\n",
"\n",
"anabolism['purR'] = {\n",
" \"macromolecular_synthesis\": ['mnmC','ppiA','sirA'],\n",
" \"biosynthesis\": {\n",
" \"carbohydrate\": [],\n",
" \"nucleotides\": ['purC','purE','purF','purK','purL','purM','purN','purT','ubiX','guaB',\n",
" 'glyA','purD','purH','pyrI','pyrB','pyrL'],\n",
" \"amino_acids\": ['carA','carB'],\n",
" \"lipids\": ['fabB',]\n",
" },\n",
" \"accessory\": ['fhuC','fhuD','fhuB'],\n",
" \"regulators\": []\n",
" }\n",
"\n",
"chemiosmosis['purR'] = {\n",
" \"ETC\": {\n",
" \"dehydrogenases\": [],\n",
" \"oxidoreductases\": [],\n",
" \"accessory\": []\n",
" },\n",
" \"fermentation\": [],\n",
" \"ion_pumps\": [],\n",
" \"motility\": [],\n",
" \"regulators\": ['gadX']\n",
" }\n",
"\n",
"unclassified['purR'] = ['ydiJ','yebG','yohH','cvpA','yfgO','yfgC','yfgD','ssnA','ygfT','yhhQ','ryjA']"
],
"language": "python",
"metadata": {},
"outputs": [],
"prompt_number": 110
},
{
"cell_type": "heading",
"level": 1,
"metadata": {},
"source": [
"ArgR"
]
},
{
"cell_type": "code",
"collapsed": false,
"input": [
"catabolism['argR'] = {\n",
" \"transport\": {\n",
" \"carbohydrate\": ['hcaT'],\n",
" \"amino_acid\": ['aroP','dtpD','potF','potG','potH','potI','artJ','artM','artQ','artI','artP','ybjE',\n",
" 'ydgI','hisJ','hisQ','hisM','hisP'],\n",
" \"nucleotides\": [],\n",
" \"lipids\": []\n",
" },\n",
" \"recycling\": {\n",
" \"carbohydrate\": ['hchA','eutM','eutD','eutT','eutQ','eutP','eutS','glmM','gph','phnO','phnB','phnS'],\n",
" \"amino_acid\": ['puuB','puuE','astE','astB','astD','astA','astC'],\n",
" \"lipids\": ['dapE'],\n",
" \"nucleotides\": []\n",
" },\n",
" \"glycolysis\": ['pfkB','rpe',],\n",
" \"TCA\": [],\n",
" \"accessory\": [],\n",
" \"regulators\": {\n",
" \"carbohydrate\": ['galS']\n",
" }\n",
" }\n",
"\n",
"anabolism['argR'] = {\n",
" \"macromolecular_synthesis\": ['asnT','trpS'],\n",
" \"biosynthesis\": {\n",
" \"carbohydrate\": ['folM','mreD','mreC','mreB'],\n",
" \"nucleotides\": ['yeaJ','ubiX','purF','pyrI','pyrL','pyrB'],\n",
" \"amino_acids\": ['carA','carB','argF','hisG','hisD','hisC','hisB','hisA','hisF','hisI','argA',\n",
" 'argG','gltB','gltD','gltF','argD','aroB','aroK','argE','argC','argB','argH',\n",
" ],\n",
" \"lipids\": ['plsC','waaK','rfaZ','waaY','waaJ','waaI','waaB','rfaS','waaP','waaG','waaQ']\n",
" },\n",
" \"accessory\": [],\n",
" \"regulators\": ['crl','ftsZ','dps','mukE','mukB','ycbW','hisL','stpA','dam','damX',]\n",
" }\n",
"\n",
"chemiosmosis['argR'] = {\n",
" \"ETC\": {\n",
" \"dehydrogenases\": [],\n",
" \"oxidoreductases\": [],\n",
" \"accessory\": ['trxB']\n",
" },\n",
" \"ATP synthase\": ['atpC','atpD','atpG','atpA','atpH','atpF','atpE','atpB','atpI'],\n",
" \"fermentation\": [],\n",
" \"ion_pumps\": [],\n",
" \"motility\": [],\n",
" \"regulators\": ['narL']\n",
" }\n",
"\n",
"unclassified['argR'] = ['yaaU','ykgA','yahA','dacC','ycbU','ycbF','ycbV','ycfD','isrA','ydeN','yoaI','yeaL',\n",
" 'yoeI','yfcC','cvpA','yffL','yffB','ypfN','yqaE','yraQ']"
],
"language": "python",
"metadata": {},
"outputs": [],
"prompt_number": 111
},
{
"cell_type": "heading",
"level": 1,
"metadata": {},
"source": [
"Cra"
]
},
{
"cell_type": "code",
"collapsed": false,
"input": [
"catabolism['cra'] = {\n",
" \"transport\": {\n",
" \"carbohydrate\": ['manY','fruA','fruB','ptsH'],\n",
" \"amino_acid\": [],\n",
" \"nucleotides\": [],\n",
" \"lipids\": []\n",
" },\n",
" \"recycling\": {\n",
" \"carbohydrate\": ['fruK','mtlD','envC'],\n",
" \"amino_acid\": [],\n",
" \"lipids\": [],\n",
" \"nucleotides\": []\n",
" },\n",
" \"glycolysis\": ['dhaM','dhaL','dhaK','dhaK','pykF','ppsA','ppsR','gapA','glk','eno','fbaA','pgk',\n",
" 'gpmM','pfkA','tpiA','fbp'],\n",
" \"TCA\": ['sucB','icd','aceB','aceK'],\n",
" \"accessory\": [],\n",
" \"regulators\": {\n",
" \"carbohydrate\": ['dhaR','crr']\n",
" }\n",
" }\n",
"\n",
"anabolism['cra'] = {\n",
" \"macromolecular_synthesis\": ['rpoS',],\n",
" \"biosynthesis\": {\n",
" \"carbohydrate\": [],\n",
" \"nucleotides\": ['pntA','epd'],\n",
" \"amino_acids\": ['carA','leuD','leuC','leuB','leuA'],\n",
" \"lipids\": []\n",
" },\n",
" \"accessory\": [],\n",
" \"regulators\": []\n",
" }\n",
"\n",
"chemiosmosis['cra'] = {\n",
" \"ETC\": {\n",
" \"dehydrogenases\": ['nuoA','nuoB','nuoC','nuoE','nuoF','nuoK'],\n",
" \"oxidoreductases\": ['cyoD','cyoC','cyoE','nirD'],\n",
" \"accessory\": ['msrB']\n",
" },\n",
" \"fermentation\": ['adhE'],\n",
" \"ion_pumps\": [],\n",
" \"motility\": [],\n",
" \"regulators\": []\n",
" }\n",
"\n",
"global_regs['cra'] = ['pdhR','crp']\n",
"unclassified['cra'] = ['ydgH','yeaC','yeaD']"
],
"language": "python",
"metadata": {},
"outputs": [],
"prompt_number": 112
},
{
"cell_type": "heading",
"level": 1,
"metadata": {},
"source": [
"PdhR"
]
},
{
"cell_type": "code",
"collapsed": false,
"input": [
"catabolism['pdhR'] = {\n",
" \"transport\": {\n",
" \"carbohydrate\": ['ygaH','glcA','ynfM'],\n",
" \"amino_acid\": [],\n",
" \"nucleotides\": [],\n",
" \"lipids\": []\n",
" },\n",
" \"recycling\": {\n",
" \"carbohydrate\": ['ybiV','prpC','prpB'],\n",
" \"amino_acid\": [],\n",
" \"lipids\": [],\n",
" \"nucleotides\": ['hpt','envC']\n",
" },\n",
" \"glycolysis\": ['aceE','aceF','lpd','yfiD'],\n",
" \"TCA\": ['glcD','glcB','glcG','glcF'],\n",
" \"accessory\": [],\n",
" \"regulators\": {\n",
" \"carbohydrate\": []\n",
" }\n",
" }\n",
"\n",
"anabolism['pdhR'] = {\n",
" \"macromolecular_synthesis\": ['tig'],\n",
" \"biosynthesis\": {\n",
" \"carbohydrate\": ['murC','murD','murE','murG','mraY'],\n",
" \"nucleotides\": [],\n",
" \"amino_acids\": ['aroF','tyrA','metB'],\n",
" \"accessory\": ['fecA','fecB','fecC','fecD','fecE'],\n",
" \"lipids\": ['lipA']\n",
" },\n",
" \"accessory\": [],\n",
" \"regulators\": ['ftsW','ftsI','ftsL','dnaB','mraW','metR']\n",
" }\n",
"\n",
"chemiosmosis['pdhR'] = {\n",
" \"ETC\": {\n",
" \"dehydrogenases\": ['ndh','glpD'],\n",
" \"oxidoreductases\": ['cyoA','cyoB','cyoC','cyoD','cyoE'],\n",
" \"accessory\": ['hemL']\n",
" },\n",
" \"fermentation\": [],\n",
" \"ion_pumps\": [],\n",
" \"motility\": [],\n",
" \"regulators\": []\n",
" }\n",
"\n",
"global_regs['pdhR'] = ['pdhR']\n",
"unclassified['pdhR'] = ['hha','tomB','yfgH','yhjX']"
],
"language": "python",
"metadata": {},
"outputs": [],
"prompt_number": 113
},
{
"cell_type": "heading",
"level": 1,
"metadata": {},
"source": [
"NarL"
]
},
{
"cell_type": "code",
"collapsed": false,
"input": [
"catabolism['narL'] = {\n",
" \"transport\": {\n",
" \"carbohydrate\": ['dcuA','dcuB'],\n",
" \"amino_acid\": [],\n",
" \"nucleotides\": [],\n",
" \"lipids\": []\n",
" },\n",
" \"recycling\": {\n",
" \"carbohydrate\": [],\n",
" \"amino_acid\": [],\n",
" \"lipids\": [],\n",
" \"nucleotides\": []\n",
" },\n",
" \"glycolysis\": ['pflB'],\n",
" \"TCA\": ['aspA','fumB'],\n",
" \"accessory\": [],\n",
" \"regulators\": {\n",
" \"carbohydrate\": ['caiF','dcuR','dcuS']\n",
" }\n",
" }\n",
"\n",
"anabolism['narL'] = {\n",
" \"macromolecular_synthesis\": [],\n",
" \"biosynthesis\": {\n",
" \"carbohydrate\": [],\n",
" \"nucleotides\": ['ubiA','ubiC'],\n",
" \"amino_acids\": [],\n",
" \"lipids\": []\n",
" },\n",
" \"accessory\": [],\n",
" \"regulators\": []\n",
" }\n",
"\n",
"chemiosmosis['narL'] = {\n",
" \"ETC\": {\n",
" \"dehydrogenases\": ['fdhF','fdnG','fdnH','fdnI','hyaA','hyaB','hyaC','hyaD','hyaE','hyaF',\n",
" 'hybA','hybB','hybC','hybD','hybE','hybF','hybG','hybO','nuoA','nuoB',\n",
" 'nuoC','nuoD','nuoE','nuoF','nuoG','nuoH','nuoI','nuoJ','nuoK','nuoL',\n",
" 'nuoM','nuoN','torA','torC','torD','ydhT','ydhU','ydhV','ydhW','ydhX',\n",
" 'ydhY'],\n",
" \"oxidoreductases\": ['napB','dmsA','dmsB','dmsC','dmsD','frdA','frdB','frdC','frdD','hcr',\n",
" 'napA','napC','napD','napF','napG','napH','narG','narH','narI','nirB',\n",
" 'nirC','nirD','nrfA','nrfB','nrfC','nrfD','nrfE','nrfF','nrfG',],\n",
" \"accessory\": ['ccmA','ccmB','ccmC','ccmD','ccmE','ccmF','ccmG','ccmH','cysG','hcp',\n",
" 'moeA','moeB','nikA','nikB','nikC','nikD','nikE','norV','norW','ynfE',\n",
" 'ynfF','ynfG','ynfH','ytfE']\n",
" },\n",
" \"fermentation\": ['adhE','focA'],\n",
" \"ion_pumps\": ['cydD','cydC','narJ','narK'],\n",
" \"motility\": [],\n",
" \"regulators\": ['nikR']\n",
" }\n",
"\n",
"unclassified['narL'] = ['ogt','yeaR','yoaG']"
],
"language": "python",
"metadata": {},
"outputs": [],
"prompt_number": 114
},
{
"cell_type": "heading",
"level": 1,
"metadata": {},
"source": [
"TrpR"
]
},
{
"cell_type": "code",
"collapsed": false,
"input": [
"catabolism['trpR'] = {\n",
" \"transport\": {\n",
" \"carbohydrate\": [],\n",
" \"amino_acid\": ['mtr'],\n",
" \"nucleotides\": [],\n",
" \"lipids\": []\n",
" },\n",
" \"recycling\": {\n",
" \"carbohydrate\": [],\n",
" \"amino_acid\": [],\n",
" \"lipids\": [],\n",
" \"nucleotides\": []\n",
" },\n",
" \"glycolysis\": [],\n",
" \"TCA\": [],\n",
" \"accessory\": [],\n",
" \"regulators\": {\n",
" \"carbohydrate\": []\n",
" }\n",
" }\n",
"\n",
"anabolism['trpR'] = {\n",
" \"macromolecular_synthesis\": [],\n",
" \"biosynthesis\": {\n",
" \"carbohydrate\": [],\n",
" \"nucleotides\": [],\n",
" \"amino_acids\": ['aroL','aroM','trpE','trpD','trpC','trpB','trpA','aroH'],\n",
" \"lipids\": []\n",
" },\n",
" \"accessory\": ['fhuC','fhuD','fhuB'],\n",
" \"regulators\": ['trpL','trpR']\n",
" }\n",
"\n",
"\n",
"unclassified['trpR'] = ['yaiA','ftnB','mdtL']"
],
"language": "python",
"metadata": {},
"outputs": [],
"prompt_number": 115
},
{
"cell_type": "heading",
"level": 1,
"metadata": {},
"source": [
"AppY"
]
},
{
"cell_type": "code",
"collapsed": false,
"input": [
"chemiosmosis['appY'] = {\n",
" \"ETC\": {\n",
" \"dehydrogenases\": ['hyaA','hyaB','hyaC','hyaD','hyaE','hyaF'],\n",
" \"oxidoreductases\": ['appB','appC'],\n",
" \"accessory\": []\n",
" },\n",
" \"fermentation\": [],\n",
" \"pH\": ['appA'],\n",
" \"ion_pumps\": [],\n",
" \"motility\": [],\n",
" \"regulators\": []\n",
" }\n",
"\n",
"unclassified['appY'] = ['yccB']"
],
"language": "python",
"metadata": {},
"outputs": [],
"prompt_number": 116
},
{
"cell_type": "heading",
"level": 1,
"metadata": {},
"source": [
"RutR"
]
},
{
"cell_type": "code",
"collapsed": false,
"input": [
"catabolism['rutR'] = {\n",
" \"transport\": {\n",
" \"carbohydrate\": [],\n",
" \"amino_acid\": [],\n",
" \"nucleotides\": ['rutG'],\n",
" \"lipids\": []\n",
" },\n",
" \"recycling\": {\n",
" \"carbohydrate\": [],\n",
" \"amino_acid\": ['nemA'],\n",
" \"lipids\": [],\n",
" \"nucleotides\": ['rutA','rutB','rutC','rutD','rutE','rutF']\n",
" },\n",
" \"glycolysis\": [],\n",
" \"TCA\": [],\n",
" \"accessory\": [],\n",
" \"regulators\": {\n",
" \"carbohydrate\": ['nemR']\n",
" }\n",
" }\n",
"\n",
"anabolism['rutR'] = {\n",
" \"macromolecular_synthesis\": [],\n",
" \"biosynthesis\": {\n",
" \"carbohydrate\": [],\n",
" \"nucleotides\": [],\n",
" \"amino_acids\": ['carA','carB'],\n",
" \"lipids\": []\n",
" },\n",
" \"accessory\": ['fepB'],\n",
" \"regulators\": ['gmr']\n",
" }\n",
"\n",
"chemiosmosis['rutR'] = {\n",
" \"ETC\": {\n",
" \"dehydrogenases\": [],\n",
" \"oxidoreductases\": [],\n",
" \"accessory\": []\n",
" },\n",
" \"fermentation\": [],\n",
" \"ion_pumps\": [],\n",
" \"motility\": [],\n",
" \"regulators\": ['gadW','gadX']\n",
" }\n",
"\n",
"unclassified['rutR'] = []"
],
"language": "python",
"metadata": {},
"outputs": [],
"prompt_number": 117
},
{
"cell_type": "heading",
"level": 1,
"metadata": {},
"source": [
"CytR"
]
},
{
"cell_type": "code",
"collapsed": false,
"input": [
"catabolism['cytR'] = {\n",
" \"transport\": {\n",
" \"carbohydrate\": [],\n",
" \"amino_acid\": [],\n",
" \"nucleotides\": ['nupC','nupG','tsx'],\n",
" \"lipids\": []\n",
" },\n",
" \"recycling\": {\n",
" \"carbohydrate\": [],\n",
" \"amino_acid\": ['cdd'],\n",
" \"lipids\": [],\n",
" \"nucleotides\": ['deoA','deoB','deoC','deoD','udp']\n",
" },\n",
" \"glycolysis\": [],\n",
" \"TCA\": [],\n",
" \"accessory\": [],\n",
" \"regulators\": {\n",
" \"carbohydrate\": []\n",
" }\n",
" }\n",
"\n",
"anabolism['cytR'] = {\n",
" \"macromolecular_synthesis\": ['ppiA','rpoH'],\n",
" \"biosynthesis\": {\n",
" \"carbohydrate\": [],\n",
" \"nucleotides\": [],\n",
" \"amino_acids\": [],\n",
" \"lipids\": []\n",
" },\n",
" \"accessory\": [],\n",
" \"regulators\": []\n",
" }\n"
],
"language": "python",
"metadata": {},
"outputs": [],
"prompt_number": 118
},
{
"cell_type": "heading",
"level": 1,
"metadata": {},
"source": [
"AllR"
]
},
{
"cell_type": "code",
"collapsed": false,
"input": [
"catabolism['allR'] = {\n",
" \"transport\": {\n",
" \"carbohydrate\": [],\n",
" \"amino_acid\": [],\n",
" \"nucleotides\": ['ybbW','ybbY'],\n",
" \"lipids\": []\n",
" },\n",
" \"recycling\": {\n",
" \"carbohydrate\": ['allA','allB','gcl','glxK','hyi'],\n",
" \"amino_acid\": [],\n",
" \"lipids\": [],\n",
" \"nucleotides\": []\n",
" },\n",
" \"glycolysis\": [],\n",
" \"TCA\": [],\n",
" \"accessory\": [],\n",
" \"regulators\": {\n",
" \"carbohydrate\": ['allS']\n",
" }\n",
" }"
],
"language": "python",
"metadata": {},
"outputs": [],
"prompt_number": 119
},
{
"cell_type": "heading",
"level": 1,
"metadata": {},
"source": [
"AllS"
]
},
{
"cell_type": "code",
"collapsed": false,
"input": [
"catabolism['allS'] = {\n",
" \"transport\": {\n",
" \"carbohydrate\": [],\n",
" \"amino_acid\": [],\n",
" \"nucleotides\": [],\n",
" \"lipids\": []\n",
" },\n",
" \"recycling\": {\n",
" \"carbohydrate\": ['allC','allD','allE'],\n",
" \"amino_acid\": [],\n",
" \"lipids\": [],\n",
" \"nucleotides\": []\n",
" },\n",
" \"glycolysis\": [],\n",
" \"TCA\": [],\n",
" \"accessory\": [],\n",
" \"regulators\": {\n",
" \"carbohydrate\": []\n",
" }\n",
" }"
],
"language": "python",
"metadata": {},
"outputs": [],
"prompt_number": 120
},
{
"cell_type": "heading",
"level": 1,
"metadata": {},
"source": [
"AraC"
]
},
{
"cell_type": "code",
"collapsed": false,
"input": [
"catabolism['araC'] = {\n",
" \"transport\": {\n",
" \"carbohydrate\": ['araE','araF','araG','araH'],\n",
" \"amino_acid\": [],\n",
" \"nucleotides\": [],\n",
" \"lipids\": []\n",
" },\n",
" \"recycling\": {\n",
" \"carbohydrate\": ['araB','araA','araD','xylA','xylB'],\n",
" \"amino_acid\": [],\n",
" \"lipids\": [],\n",
" \"nucleotides\": []\n",
" },\n",
" \"glycolysis\": [],\n",
" \"TCA\": [],\n",
" \"accessory\": [],\n",
" \"regulators\": {\n",
" \"carbohydrate\": []\n",
" }\n",
" }\n",
"\n",
"unclassified['araC'] = ['araJ']"
],
"language": "python",
"metadata": {},
"outputs": [],
"prompt_number": 121
},
{
"cell_type": "heading",
"level": 1,
"metadata": {},
"source": [
"ArgP"
]
},
{
"cell_type": "code",
"collapsed": false,
"input": [
"anabolism['argP'] = {\n",
" \"macromolecular_synthesis\": ['dnaN','recF'],\n",
" \"biosynthesis\": {\n",
" \"carbohydrate\": [],\n",
" \"nucleotides\": ['nrdA','nrdB'],\n",
" \"amino_acids\": ['dapB'],\n",
" \"lipids\": []\n",
" },\n",
" \"accessory\": [],\n",
" \"regulators\": ['dnaA',]\n",
" }\n",
"\n",
"chemiosmosis['argP'] = {\n",
" \"ETC\": {\n",
" \"dehydrogenases\": [],\n",
" \"oxidoreductases\": [],\n",
" \"accessory\": []\n",
" },\n",
" \"fermentation\": [],\n",
" \"ion_pumps\": ['argO'],\n",
" \"motility\": [],\n",
" \"regulators\": []\n",
" }"
],
"language": "python",
"metadata": {},
"outputs": [],
"prompt_number": 122
},
{
"cell_type": "heading",
"level": 1,
"metadata": {},
"source": [
"AsnC"
]
},
{
"cell_type": "code",
"collapsed": false,
"input": [
"anabolism['asnC'] = {\n",
" \"macromolecular_synthesis\": ['mnmG'],\n",
" \"biosynthesis\": {\n",
" \"carbohydrate\": ['mioC'],\n",
" \"nucleotides\": [],\n",
" \"amino_acids\": ['asnA'],\n",
" \"lipids\": []\n",
" },\n",
" \"accessory\": [],\n",
" \"regulators\": []\n",
" }"
],
"language": "python",
"metadata": {},
"outputs": [],
"prompt_number": 123
},
{
"cell_type": "heading",
"level": 1,
"metadata": {},
"source": [
"BetI"
]
},
{
"cell_type": "code",
"collapsed": false,
"input": [
"catabolism['betI'] = {\n",
" \"transport\": {\n",
" \"carbohydrate\": [],\n",
" \"amino_acid\": ['betT'],\n",
" \"nucleotides\": [],\n",
" \"lipids\": []\n",
" }\n",
" \n",
" }\n",
"\n",
"anabolism['betI'] = {\n",
" \"macromolecular_synthesis\": [],\n",
" \"biosynthesis\": {\n",
" \"carbohydrate\": [],\n",
" \"nucleotides\": [],\n",
" \"amino_acids\": ['betA','betB'],\n",
" \"lipids\": []\n",
" },\n",
" \"accessory\": [],\n",
" \"regulators\": []\n",
" }"
],
"language": "python",
"metadata": {},
"outputs": [],
"prompt_number": 124
},
{
"cell_type": "heading",
"level": 1,
"metadata": {},
"source": [
"BirA"
]
},
{
"cell_type": "code",
"collapsed": false,
"input": [
"anabolism['birA'] = {\n",
" \"macromolecular_synthesis\": [],\n",
" \"biosynthesis\": {\n",
" \"carbohydrate\": ['bioA','bioB','bioC','bioD','bioE'],\n",
" \"nucleotides\": [],\n",
" \"amino_acids\": [],\n",
" \"lipids\": []\n",
" },\n",
" \"accessory\": [],\n",
" \"regulators\": []\n",
" }"
],
"language": "python",
"metadata": {},
"outputs": [],
"prompt_number": 125
},
{
"cell_type": "heading",
"level": 1,
"metadata": {},
"source": [
"CaiF"
]
},
{
"cell_type": "code",
"collapsed": false,
"input": [
"catabolism['caiF'] = {\n",
" \"transport\": {\n",
" \"carbohydrate\": [],\n",
" \"amino_acid\": [],\n",
" \"nucleotides\": [],\n",
" \"lipids\": []\n",
" },\n",
" \"recycling\": {\n",
" \"carbohydrate\": ['caiA','caiB','caiC','caiD','caiD','caiE'],\n",
" \"amino_acid\": [],\n",
" \"lipids\": [],\n",
" \"nucleotides\": []\n",
" },\n",
" \"glycolysis\": [],\n",
" \"TCA\": [],\n",
" \"accessory\": [],\n",
" \"regulators\": {\n",
" \"carbohydrate\": ['caiT']\n",
" }\n",
" }\n",
"\n",
"chemiosmosis['caiF'] = {\n",
" \"ETC\": {\n",
" \"dehydrogenases\": [],\n",
" \"oxidoreductases\": ['fixA','fixB','fixC','fixX'],\n",
" \"accessory\": []\n",
" },\n",
" \"fermentation\": [],\n",
" \"ion_pumps\": [],\n",
" \"motility\": [],\n",
" \"regulators\": []\n",
" }"
],
"language": "python",
"metadata": {},
"outputs": [],
"prompt_number": 126
},
{
"cell_type": "heading",
"level": 1,
"metadata": {},
"source": [
"CdaR"
]
},
{
"cell_type": "code",
"collapsed": false,
"input": [
"catabolism['cdaR'] = {\n",
" \"transport\": {\n",
" \"carbohydrate\": ['garP','gudP'],\n",
" \"amino_acid\": [],\n",
" \"nucleotides\": [],\n",
" \"lipids\": []\n",
" },\n",
" \"recycling\": {\n",
" \"carbohydrate\": ['garD','garL','garR','garK','gudD','gudX'],\n",
" \"amino_acid\": [],\n",
" \"lipids\": [],\n",
" \"nucleotides\": ['rnpA']\n",
" },\n",
" \"glycolysis\": [],\n",
" \"TCA\": [],\n",
" \"accessory\": [],\n",
" \"regulators\": {\n",
" \"carbohydrate\": []\n",
" }\n",
" }"
],
"language": "python",
"metadata": {},
"outputs": [],
"prompt_number": 127
},
{
"cell_type": "heading",
"level": 1,
"metadata": {},
"source": [
"CynR"
]
},
{
"cell_type": "code",
"collapsed": false,
"input": [
"catabolism['cynR'] = {\n",
" \"transport\": {\n",
" \"carbohydrate\": ['cynX'],\n",
" \"amino_acid\": [],\n",
" \"nucleotides\": [],\n",
" \"lipids\": []\n",
" },\n",
" \"recycling\": {\n",
" \"carbohydrate\": ['cynS','cynT'],\n",
" \"amino_acid\": [],\n",
" \"lipids\": [],\n",
" \"nucleotides\": []\n",
" },\n",
" \"glycolysis\": [],\n",
" \"TCA\": [],\n",
" \"accessory\": [],\n",
" \"regulators\": {\n",
" \"carbohydrate\": []\n",
" }\n",
" }"
],
"language": "python",
"metadata": {},
"outputs": [],
"prompt_number": 128
},
{
"cell_type": "heading",
"level": 1,
"metadata": {},
"source": [
"CysB"
]
},
{
"cell_type": "code",
"collapsed": false,
"input": [
"catabolism['cysB'] = {\n",
" \"transport\": {\n",
" \"carbohydrate\": [],\n",
" \"amino_acid\": ['tauA','tauB','tauC'],\n",
" \"nucleotides\": [],\n",
" \"lipids\": [],\n",
" \"cofactors\": ['cysA','cysW','cysU','cysP','cysD','cysN','cysC','ssuA','ssuB','ssuC']\n",
" },\n",
" \"recycling\": {\n",
" \"carbohydrate\": ['ssuD','ssuE'],\n",
" \"amino_acid\": ['cysA','cysJ','cysI','cysH','cysK','cysM','tauD'],\n",
" \"lipids\": [],\n",
" \"nucleotides\": []\n",
" },\n",
" \"glycolysis\": [],\n",
" \"TCA\": [],\n",
" \"accessory\": [],\n",
" \"regulators\": {\n",
" \"carbohydrate\": [],\n",
" \"cofactors\": ['cbl']\n",
" }\n",
" }\n",
"\n",
"unclassified['cysB'] = ['hslJ']"
],
"language": "python",
"metadata": {},
"outputs": [],
"prompt_number": 129
},
{
"cell_type": "heading",
"level": 1,
"metadata": {},
"source": [
"DcuR"
]
},
{
"cell_type": "code",
"collapsed": false,
"input": [
"catabolism['dcuR'] = {\n",
" \"transport\": {\n",
" \"carbohydrate\": ['dctA','dcuB'],\n",
" \"amino_acid\": [],\n",
" \"nucleotides\": [],\n",
" \"lipids\": []\n",
" },\n",
" \"recycling\": {\n",
" \"carbohydrate\": [],\n",
" \"amino_acid\": [],\n",
" \"lipids\": [],\n",
" \"nucleotides\": []\n",
" },\n",
" \"glycolysis\": [],\n",
" \"TCA\": ['fumB'],\n",
" \"accessory\": [],\n",
" \"regulators\": {\n",
" \"carbohydrate\": []\n",
" }\n",
" }\n",
"\n",
"chemiosmosis['dcuR'] = {\n",
" \"ETC\": {\n",
" \"dehydrogenases\": [],\n",
" \"oxidoreductases\": ['frdA','frdB','frdC','frdD'],\n",
" \"accessory\": []\n",
" },\n",
" \"fermentation\": [],\n",
" \"ion_pumps\": [],\n",
" \"motility\": [],\n",
" \"regulators\": []\n",
" }"
],
"language": "python",
"metadata": {},
"outputs": [],
"prompt_number": 130
},
{
"cell_type": "heading",
"level": 1,
"metadata": {},
"source": [
"DeoR"
]
},
{
"cell_type": "code",
"collapsed": false,
"input": [
"catabolism['deoR'] = {\n",
" \"transport\": {\n",
" \"carbohydrate\": [],\n",
" \"amino_acid\": [],\n",
" \"nucleotides\": ['nupG','tsx'],\n",
" \"lipids\": []\n",
" },\n",
" \"recycling\": {\n",
" \"carbohydrate\": [],\n",
" \"amino_acid\": [],\n",
" \"lipids\": [],\n",
" \"nucleotides\": ['deoA','deoB','deoC','deoD',]\n",
" },\n",
" \"glycolysis\": [],\n",
" \"TCA\": [],\n",
" \"accessory\": [],\n",
" \"regulators\": {\n",
" \"carbohydrate\": []\n",
" }\n",
" }\n"
],
"language": "python",
"metadata": {},
"outputs": [],
"prompt_number": 131
},
{
"cell_type": "heading",
"level": 1,
"metadata": {},
"source": [
"DhaR"
]
},
{
"cell_type": "code",
"collapsed": false,
"input": [
"catabolism['dhaR'] = {\n",
" \"transport\": {\n",
" \"carbohydrate\": [],\n",
" \"amino_acid\": [],\n",
" \"nucleotides\": [],\n",
" \"lipids\": []\n",
" },\n",
" \"recycling\": {\n",
" \"carbohydrate\": [],\n",
" \"amino_acid\": [],\n",
" \"lipids\": [],\n",
" \"nucleotides\": []\n",
" },\n",
" \"glycolysis\": ['dhaK','dhaL','dhaM'],\n",
" \"TCA\": [],\n",
" \"accessory\": [],\n",
" \"regulators\": {\n",
" \"carbohydrate\": []\n",
" }\n",
" }"
],
"language": "python",
"metadata": {},
"outputs": [],
"prompt_number": 132
},
{
"cell_type": "heading",
"level": 1,
"metadata": {},
"source": [
"DnaA"
]
},
{
"cell_type": "code",
"collapsed": false,
"input": [
"catabolism['dnaA'] = {\n",
" \"transport\": {\n",
" \"carbohydrate\": [],\n",
" \"amino_acid\": [],\n",
" \"nucleotides\": [],\n",
" \"lipids\": []\n",
" },\n",
" \"recycling\": {\n",
" \"carbohydrate\": [],\n",
" \"amino_acid\": [],\n",
" \"lipids\": [],\n",
" \"nucleotides\": []\n",
" },\n",
" \"glycolysis\": [],\n",
" \"TCA\": ['aldA'],\n",
" \"accessory\": [],\n",
" \"regulators\": {\n",
" \"carbohydrate\": []\n",
" }\n",
" }\n",
"\n",
"anabolism['dnaA'] = {\n",
" \"macromolecular_synthesis\": ['dnaN','nrdA','nrdB','polA','recF','rpoH'],\n",
" \"biosynthesis\": {\n",
" \"carbohydrate\": [],\n",
" \"nucleotides\": ['guaA','guaB'],\n",
" \"amino_acids\": [],\n",
" \"lipids\": []\n",
" },\n",
" \"accessory\": [],\n",
" \"regulators\": []\n",
" }\n",
"\n",
"unclassified['dnaA'] = ['yjeV']"
],
"language": "python",
"metadata": {},
"outputs": [],
"prompt_number": 133
},
{
"cell_type": "heading",
"level": 1,
"metadata": {},
"source": [
"DpiA"
]
},
{
"cell_type": "code",
"collapsed": false,
"input": [
"catabolism['dpiA'] = {\n",
" \"transport\": {\n",
" \"carbohydrate\": ['exuT'],\n",
" \"amino_acid\": [],\n",
" \"nucleotides\": [],\n",
" \"lipids\": []\n",
" },\n",
" \"recycling\": {\n",
" \"carbohydrate\": [],\n",
" \"amino_acid\": [],\n",
" \"lipids\": [],\n",
" \"nucleotides\": []\n",
" },\n",
" \"glycolysis\": [],\n",
" \"TCA\": ['mdh'],\n",
" \"accessory\": [],\n",
" \"regulators\": {\n",
" \"carbohydrate\": []\n",
" }\n",
" }\n",
"\n",
"\n",
"anabolism['dpiA'] = {\n",
" \"macromolecular_synthesis\": [],\n",
" \"biosynthesis\": {\n",
" \"carbohydrate\": ['citC','citD','citE','citF','citG','citX'],\n",
" \"nucleotides\": [],\n",
" \"amino_acids\": [],\n",
" \"lipids\": []\n",
" },\n",
" \"accessory\": [],\n",
" \"regulators\": ['dpiA','dpiB']\n",
" }\n",
"\n",
"\n",
"chemiosmosis['dpiA'] = {\n",
" \"ETC\": {\n",
" \"dehydrogenases\": [],\n",
" \"oxidoreductases\": [],\n",
" \"accessory\": []\n",
" },\n",
" \"fermentation\": [],\n",
" \"ion_pumps\": [],\n",
" \"motility\": [],\n",
" \"regulators\": ['appY']\n",
" }"
],
"language": "python",
"metadata": {},
"outputs": [],
"prompt_number": 134
},
{
"cell_type": "heading",
"level": 1,
"metadata": {},
"source": [
"DsdC"
]
},
{
"cell_type": "code",
"collapsed": false,
"input": [
"catabolism['dsdC'] = {\n",
" \"transport\": {\n",
" \"carbohydrate\": [],\n",
" \"amino_acid\": ['dsdX'],\n",
" \"nucleotides\": [],\n",
" \"lipids\": []\n",
" },\n",
" \"recycling\": {\n",
" \"carbohydrate\": [],\n",
" \"amino_acid\": ['dsdA'],\n",
" \"lipids\": [],\n",
" \"nucleotides\": []\n",
" },\n",
" \"glycolysis\": [],\n",
" \"TCA\": [],\n",
" \"accessory\": [],\n",
" \"regulators\": {\n",
" \"carbohydrate\": []\n",
" }\n",
" }"
],
"language": "python",
"metadata": {},
"outputs": [],
"prompt_number": 135
},
{
"cell_type": "heading",
"level": 1,
"metadata": {},
"source": [
"FabR"
]
},
{
"cell_type": "code",
"collapsed": false,
"input": [
"anabolism['fabR'] = {\n",
" \"macromolecular_synthesis\": [],\n",
" \"biosynthesis\": {\n",
" \"carbohydrate\": [],\n",
" \"nucleotides\": [],\n",
" \"amino_acids\": [],\n",
" \"lipids\": ['fabA','fabB']\n",
" },\n",
" \"accessory\": [],\n",
" \"regulators\": []\n",
" }"
],
"language": "python",
"metadata": {},
"outputs": [],
"prompt_number": 136
},
{
"cell_type": "heading",
"level": 1,
"metadata": {},
"source": [
"FadR"
]
},
{
"cell_type": "code",
"collapsed": false,
"input": [
"catabolism['fadR'] = {\n",
" \"transport\": {\n",
" \"carbohydrate\": [],\n",
" \"amino_acid\": [],\n",
" \"nucleotides\": [],\n",
" \"lipids\": ['fadD','fadL']\n",
" },\n",
" \"recycling\": {\n",
" \"carbohydrate\": [],\n",
" \"amino_acid\": [],\n",
" \"lipids\": ['fadA','fadB','fadC','fadE','fadH','fadI','fadJ'],\n",
" \"nucleotides\": []\n",
" },\n",
" \"glycolysis\": [],\n",
" \"TCA\": [],\n",
" \"accessory\": [],\n",
" \"regulators\": {\n",
" \"carbohydrate\": ['iclR']\n",
" }\n",
" }\n",
"\n",
"\n",
"anabolism['fadR'] = {\n",
" \"macromolecular_synthesis\": [],\n",
" \"biosynthesis\": {\n",
" \"carbohydrate\": [],\n",
" \"nucleotides\": [],\n",
" \"amino_acids\": [],\n",
" \"lipids\": []\n",
" },\n",
" \"accessory\": [],\n",
" \"regulators\": ['uspA']\n",
" }"
],
"language": "python",
"metadata": {},
"outputs": [],
"prompt_number": 137
},
{
"cell_type": "heading",
"level": 1,
"metadata": {},
"source": [
"FhlA"
]
},
{
"cell_type": "code",
"collapsed": false,
"input": [
"chemiosmosis['fhlA'] = {\n",
" \"ETC\": {\n",
" \"dehydrogenases\": ['fdhF','hycB','hycC','hycD','hycE','hycF','hycG','hydN',\n",
" 'hyfA','hyfB','hyfG','hyfI','hyfC','hyfD','hyfE','hyfF',\n",
" 'hyfH','hypA','hypB'],\n",
" \"oxidoreductases\": [],\n",
" \"accessory\": ['hycH','hycI','hyfJ','hypC','hypD','hypE','hypF']\n",
" },\n",
" \"fermentation\": ['focB'],\n",
" \"ion_pumps\": [],\n",
" \"motility\": [],\n",
" \"regulators\": ['hycA','hyfR']\n",
" }\n"
],
"language": "python",
"metadata": {},
"outputs": [],
"prompt_number": 138
},
{
"cell_type": "heading",
"level": 1,
"metadata": {},
"source": [
"GalR"
]
},
{
"cell_type": "code",
"collapsed": false,
"input": [
"catabolism['galR'] = {\n",
" \"transport\": {\n",
" \"carbohydrate\": ['mglA','mglB','mglC','galP'],\n",
" \"amino_acid\": [],\n",
" \"nucleotides\": [],\n",
" \"lipids\": []\n",
" },\n",
" \"recycling\": {\n",
" \"carbohydrate\": ['galE','galT','galK','galM'],\n",
" \"amino_acid\": [],\n",
" \"lipids\": [],\n",
" \"nucleotides\": []\n",
" },\n",
" \"glycolysis\": [],\n",
" \"TCA\": [],\n",
" \"accessory\": [],\n",
" \"regulators\": {\n",
" \"carbohydrate\": ['galS']\n",
" }\n",
" }"
],
"language": "python",
"metadata": {},
"outputs": [],
"prompt_number": 139
},
{
"cell_type": "heading",
"level": 1,
"metadata": {},
"source": [
"GalS"
]
},
{
"cell_type": "code",
"collapsed": false,
"input": [
"catabolism['galS'] = {\n",
" \"transport\": {\n",
" \"carbohydrate\": ['mglA','mglB','mglC','galP'],\n",
" \"amino_acid\": [],\n",
" \"nucleotides\": [],\n",
" \"lipids\": []\n",
" },\n",
" \"recycling\": {\n",
" \"carbohydrate\": ['galE','galT','galK','galM'],\n",
" \"amino_acid\": [],\n",
" \"lipids\": [],\n",
" \"nucleotides\": []\n",
" },\n",
" \"glycolysis\": [],\n",
" \"TCA\": [],\n",
" \"accessory\": [],\n",
" \"regulators\": {\n",
" \"carbohydrate\": ['galR']\n",
" }\n",
" }"
],
"language": "python",
"metadata": {},
"outputs": [],
"prompt_number": 140
},
{
"cell_type": "heading",
"level": 1,
"metadata": {},
"source": [
"GcvA"
]
},
{
"cell_type": "code",
"collapsed": false,
"input": [
"catabolism['gcvA'] = {\n",
" \"transport\": {\n",
" \"carbohydrate\": [],\n",
" \"amino_acid\": [],\n",
" \"nucleotides\": [],\n",
" \"lipids\": []\n",
" },\n",
" \"recycling\": {\n",
" \"carbohydrate\": [],\n",
" \"amino_acid\": ['gcvP','gcvH','gcvT','gcvA','gcvB'],\n",
" \"lipids\": [],\n",
" \"nucleotides\": []\n",
" },\n",
" \"glycolysis\": [],\n",
" \"TCA\": [],\n",
" \"accessory\": [],\n",
" \"regulators\": {\n",
" \"carbohydrate\": []\n",
" }\n",
" }"
],
"language": "python",
"metadata": {},
"outputs": [],
"prompt_number": 141
},
{
"cell_type": "heading",
"level": 1,
"metadata": {},
"source": [
"GlcC"
]
},
{
"cell_type": "code",
"collapsed": false,
"input": [
"catabolism['glcC'] = {\n",
" \"transport\": {\n",
" \"carbohydrate\": ['glcA'],\n",
" \"amino_acid\": [],\n",
" \"nucleotides\": [],\n",
" \"lipids\": []\n",
" },\n",
" \"recycling\": {\n",
" \"carbohydrate\": [],\n",
" \"amino_acid\": [],\n",
" \"lipids\": [],\n",
" \"nucleotides\": []\n",
" },\n",
" \"glycolysis\": [],\n",
" \"TCA\": ['glcD','glcE','gclF','glcB','glcG'],\n",
" \"accessory\": [],\n",
" \"regulators\": {\n",
" \"carbohydrate\": []\n",
" }\n",
" }"
],
"language": "python",
"metadata": {},
"outputs": [],
"prompt_number": 142
},
{
"cell_type": "heading",
"level": 1,
"metadata": {},
"source": [
"GlpR"
]
},
{
"cell_type": "code",
"collapsed": false,
"input": [
"catabolism['glpR'] = {\n",
" \"transport\": {\n",
" \"carbohydrate\": ['glpF'],\n",
" \"amino_acid\": [],\n",
" \"nucleotides\": [],\n",
" \"lipids\": []\n",
" },\n",
" \"recycling\": {\n",
" \"carbohydrate\": ['glpQ','glpT','glpX','glpK'],\n",
" \"amino_acid\": [],\n",
" \"lipids\": [],\n",
" \"nucleotides\": []\n",
" },\n",
" \"glycolysis\": [],\n",
" \"TCA\": [],\n",
" \"accessory\": [],\n",
" \"regulators\": {\n",
" \"carbohydrate\": []\n",
" }\n",
" }\n",
"\n",
"chemiosmosis['glpR'] = {\n",
" \"ETC\": {\n",
" \"dehydrogenases\": ['glpA','glpB','glpC','glpD'],\n",
" \"oxidoreductases\": [],\n",
" \"accessory\": []\n",
" },\n",
" \"fermentation\": [],\n",
" \"ion_pumps\": [],\n",
" \"motility\": [],\n",
" \"regulators\": []\n",
" }"
],
"language": "python",
"metadata": {},
"outputs": [],
"prompt_number": 143
},
{
"cell_type": "heading",
"level": 1,
"metadata": {},
"source": [
"GntR"
]
},
{
"cell_type": "code",
"collapsed": false,
"input": [
"catabolism['gntR'] = {\n",
" \"transport\": {\n",
" \"carbohydrate\": ['gntT','gntU','gntX','idnT'],\n",
" \"amino_acid\": [],\n",
" \"nucleotides\": [],\n",
" \"lipids\": []\n",
" },\n",
" \"recycling\": {\n",
" \"carbohydrate\": ['gntK','idnD','idnK','idnO'],\n",
" \"amino_acid\": [],\n",
" \"lipids\": [],\n",
" \"nucleotides\": ['nfuA']\n",
" },\n",
" \"glycolysis\": ['eda','edd'],\n",
" \"TCA\": [],\n",
" \"accessory\": [],\n",
" \"regulators\": {\n",
" \"carbohydrate\": ['idnR']\n",
" }\n",
" }"
],
"language": "python",
"metadata": {},
"outputs": [],
"prompt_number": 144
},
{
"cell_type": "heading",
"level": 1,
"metadata": {},
"source": [
"HcaR"
]
},
{
"cell_type": "code",
"collapsed": false,
"input": [
"catabolism['hcaR'] = {\n",
" \"transport\": {\n",
" \"carbohydrate\": [],\n",
" \"amino_acid\": [],\n",
" \"nucleotides\": [],\n",
" \"lipids\": []\n",
" },\n",
" \"recycling\": {\n",
" \"carbohydrate\": ['hcaB','hcaC','hcaD','hcaE','hcaF'],\n",
" \"amino_acid\": [],\n",
" \"lipids\": [],\n",
" \"nucleotides\": []\n",
" },\n",
" \"glycolysis\": [],\n",
" \"TCA\": [],\n",
" \"accessory\": [],\n",
" \"regulators\": {\n",
" \"carbohydrate\": []\n",
" }\n",
" }"
],
"language": "python",
"metadata": {},
"outputs": [],
"prompt_number": 145
},
{
"cell_type": "heading",
"level": 1,
"metadata": {},
"source": [
"IclR"
]
},
{
"cell_type": "code",
"collapsed": false,
"input": [
"catabolism['iclR'] = {\n",
" \"transport\": {\n",
" \"carbohydrate\": [],\n",
" \"amino_acid\": [],\n",
" \"nucleotides\": [],\n",
" \"lipids\": []\n",
" },\n",
" \"recycling\": {\n",
" \"carbohydrate\": [],\n",
" \"amino_acid\": [],\n",
" \"lipids\": [],\n",
" \"nucleotides\": []\n",
" },\n",
" \"glycolysis\": [],\n",
" \"TCA\": ['aceB','aceA','aceK'],\n",
" \"accessory\": [],\n",
" \"regulators\": {\n",
" \"carbohydrate\": []\n",
" }\n",
" }"
],
"language": "python",
"metadata": {},
"outputs": [],
"prompt_number": 146
},
{
"cell_type": "heading",
"level": 1,
"metadata": {},
"source": [
"IdnR"
]
},
{
"cell_type": "code",
"collapsed": false,
"input": [
"catabolism['idnR'] = {\n",
" \"transport\": {\n",
" \"carbohydrate\": ['gntU','idnT'],\n",
" \"amino_acid\": [],\n",
" \"nucleotides\": [],\n",
" \"lipids\": []\n",
" },\n",
" \"recycling\": {\n",
" \"carbohydrate\": ['gntK','idnD','idnK','idnO'],\n",
" \"amino_acid\": [],\n",
" \"lipids\": [],\n",
" \"nucleotides\": []\n",
" },\n",
" \"glycolysis\": [],\n",
" \"TCA\": [],\n",
" \"accessory\": [],\n",
" \"regulators\": {\n",
" \"carbohydrate\": []\n",
" }\n",
" }"
],
"language": "python",
"metadata": {},
"outputs": [],
"prompt_number": 147
},
{
"cell_type": "heading",
"level": 1,
"metadata": {},
"source": [
"KdgR"
]
},
{
"cell_type": "code",
"collapsed": false,
"input": [
"catabolism['kdgR'] = {\n",
" \"transport\": {\n",
" \"carbohydrate\": [],\n",
" \"amino_acid\": [],\n",
" \"nucleotides\": [],\n",
" \"lipids\": []\n",
" },\n",
" \"recycling\": {\n",
" \"carbohydrate\": [],\n",
" \"amino_acid\": [],\n",
" \"lipids\": [],\n",
" \"nucleotides\": []\n",
" },\n",
" \"glycolysis\": ['edd','eda'],\n",
" \"TCA\": [],\n",
" \"accessory\": [],\n",
" \"regulators\": {\n",
" \"carbohydrate\": []\n",
" }\n",
" }\n"
],
"language": "python",
"metadata": {},
"outputs": [],
"prompt_number": 148
},
{
"cell_type": "heading",
"level": 1,
"metadata": {},
"source": [
"LldR"
]
},
{
"cell_type": "code",
"collapsed": false,
"input": [
"catabolism['lldR'] = {\n",
" \"transport\": {\n",
" \"carbohydrate\": ['lldP'],\n",
" \"amino_acid\": [],\n",
" \"nucleotides\": [],\n",
" \"lipids\": []\n",
" },\n",
" \"recycling\": {\n",
" \"carbohydrate\": [],\n",
" \"amino_acid\": [],\n",
" \"lipids\": [],\n",
" \"nucleotides\": []\n",
" },\n",
" \"glycolysis\": [],\n",
" \"TCA\": [],\n",
" \"accessory\": [],\n",
" \"regulators\": {\n",
" \"carbohydrate\": []\n",
" }\n",
" }\n",
"\n",
"chemiosmosis['lldR'] = {\n",
" \"ETC\": {\n",
" \"dehydrogenases\": ['lldD'],\n",
" \"oxidoreductases\": [],\n",
" \"accessory\": []\n",
" },\n",
" \"fermentation\": [],\n",
" \"ion_pumps\": [],\n",
" \"motility\": [],\n",
" \"regulators\": []\n",
" }"
],
"language": "python",
"metadata": {},
"outputs": [],
"prompt_number": 149
},
{
"cell_type": "heading",
"level": 1,
"metadata": {},
"source": [
"LysR"
]
},
{
"cell_type": "code",
"collapsed": false,
"input": [
"anabolism['lysR'] = {\n",
" \"macromolecular_synthesis\": [],\n",
" \"biosynthesis\": {\n",
" \"carbohydrate\": [],\n",
" \"nucleotides\": [],\n",
" \"amino_acids\": ['lysA'],\n",
" \"lipids\": []\n",
" },\n",
" \"accessory\": [],\n",
" \"regulators\": []\n",
" }\n"
],
"language": "python",
"metadata": {},
"outputs": [],
"prompt_number": 150
},
{
"cell_type": "heading",
"level": 1,
"metadata": {},
"source": [
"MalT"
]
},
{
"cell_type": "code",
"collapsed": false,
"input": [
"catabolism['malT'] = {\n",
" \"transport\": {\n",
" \"carbohydrate\": ['malK','malF','malG','malE','lamB','malM'],\n",
" \"amino_acid\": [],\n",
" \"nucleotides\": [],\n",
" \"lipids\": []\n",
" },\n",
" \"recycling\": {\n",
" \"carbohydrate\": ['malP','malQ','malS','malZ'],\n",
" \"amino_acid\": [],\n",
" \"lipids\": [],\n",
" \"nucleotides\": []\n",
" },\n",
" \"glycolysis\": [],\n",
" \"TCA\": [],\n",
" \"accessory\": [],\n",
" \"regulators\": {\n",
" \"carbohydrate\": []\n",
" }\n",
" }\n",
"\n",
"\n",
" "
],
"language": "python",
"metadata": {},
"outputs": [],
"prompt_number": 151
},
{
"cell_type": "heading",
"level": 1,
"metadata": {},
"source": [
"MelR"
]
},
{
"cell_type": "code",
"collapsed": false,
"input": [
"catabolism['melR'] = {\n",
" \"transport\": {\n",
" \"carbohydrate\": [],\n",
" \"amino_acid\": [],\n",
" \"nucleotides\": [],\n",
" \"lipids\": []\n",
" },\n",
" \"recycling\": {\n",
" \"carbohydrate\": ['melA'],\n",
" \"amino_acid\": [],\n",
" \"lipids\": [],\n",
" \"nucleotides\": []\n",
" },\n",
" \"glycolysis\": [],\n",
" \"TCA\": [],\n",
" \"accessory\": [],\n",
" \"regulators\": {\n",
" \"carbohydrate\": []\n",
" }\n",
" }"
],
"language": "python",
"metadata": {},
"outputs": [],
"prompt_number": 152
},
{
"cell_type": "heading",
"level": 1,
"metadata": {},
"source": [
"MetJ"
]
},
{
"cell_type": "code",
"collapsed": false,
"input": [
"catabolism['metJ'] = {\n",
" \"transport\": {\n",
" \"carbohydrate\": [],\n",
" \"amino_acid\": ['metQ','metI','metN'],\n",
" \"nucleotides\": [],\n",
" \"lipids\": []\n",
" },\n",
" \"recycling\": {\n",
" \"carbohydrate\": [],\n",
" \"amino_acid\": [],\n",
" \"lipids\": [],\n",
" \"nucleotides\": []\n",
" },\n",
" \"glycolysis\": [],\n",
" \"TCA\": [],\n",
" \"accessory\": [],\n",
" \"regulators\": {\n",
" \"carbohydrate\": []\n",
" }\n",
" }\n",
"\n",
"anabolism['metJ'] = {\n",
" \"macromolecular_synthesis\": [],\n",
" \"biosynthesis\": {\n",
" \"carbohydrate\": ['folE'],\n",
" \"nucleotides\": [],\n",
" \"amino_acids\": ['metA','metB','metC','metE','metF','metK','metL'],\n",
" \"lipids\": []\n",
" },\n",
" \"accessory\": [],\n",
" \"regulators\": ['metR']\n",
" }\n",
"\n",
"unclassified['metJ'] = ['ahpC','ahpF','yeiB']"
],
"language": "python",
"metadata": {},
"outputs": [],
"prompt_number": 153
},
{
"cell_type": "heading",
"level": 1,
"metadata": {},
"source": [
"MetR"
]
},
{
"cell_type": "code",
"collapsed": false,
"input": [
"anabolism['metR'] = {\n",
" \"macromolecular_synthesis\": [],\n",
" \"biosynthesis\": {\n",
" \"carbohydrate\": [],\n",
" \"nucleotides\": ['glyA'],\n",
" \"amino_acids\": ['metA','metE','metH'],\n",
" \"lipids\": []\n",
" },\n",
" \"accessory\": [],\n",
" \"regulators\": ['metR']\n",
" }\n",
"\n",
"chemiosmosis['metR'] = {\n",
" \"ETC\": {\n",
" \"dehydrogenases\": [],\n",
" \"oxidoreductases\": [],\n",
" \"accessory\": []\n",
" },\n",
" \"fermentation\": [],\n",
" \"ion_pumps\": [],\n",
" \"motility\": [],\n",
" \"regulators\": [],\n",
" \"accessory\": ['hmp']\n",
" }\n",
"\n"
],
"language": "python",
"metadata": {},
"outputs": [],
"prompt_number": 154
},
{
"cell_type": "heading",
"level": 1,
"metadata": {},
"source": [
"MhpR"
]
},
{
"cell_type": "code",
"collapsed": false,
"input": [
"catabolism['mhpR'] = {\n",
" \"transport\": {\n",
" \"carbohydrate\": [],\n",
" \"amino_acid\": [],\n",
" \"nucleotides\": [],\n",
" \"lipids\": []\n",
" },\n",
" \"recycling\": {\n",
" \"carbohydrate\": ['mhpA','mhpB','mhpC','mhpD','mhpE','mhpF'],\n",
" \"amino_acid\": [],\n",
" \"lipids\": [],\n",
" \"nucleotides\": []\n",
" },\n",
" \"glycolysis\": [],\n",
" \"TCA\": [],\n",
" \"accessory\": [],\n",
" \"regulators\": {\n",
" \"carbohydrate\": []\n",
" }\n",
" }"
],
"language": "python",
"metadata": {},
"outputs": [],
"prompt_number": 155
},
{
"cell_type": "heading",
"level": 1,
"metadata": {},
"source": [
"MtlR"
]
},
{
"cell_type": "code",
"collapsed": false,
"input": [
"catabolism['mtlR'] = {\n",
" \"transport\": {\n",
" \"carbohydrate\": ['mtlA'],\n",
" \"amino_acid\": [],\n",
" \"nucleotides\": [],\n",
" \"lipids\": []\n",
" },\n",
" \"recycling\": {\n",
" \"carbohydrate\": ['mtlD'],\n",
" \"amino_acid\": [],\n",
" \"lipids\": [],\n",
" \"nucleotides\": []\n",
" },\n",
" \"glycolysis\": [],\n",
" \"TCA\": [],\n",
" \"accessory\": [],\n",
" \"regulators\": {\n",
" \"carbohydrate\": []\n",
" }\n",
" }"
],
"language": "python",
"metadata": {},
"outputs": [],
"prompt_number": 156
},
{
"cell_type": "heading",
"level": 1,
"metadata": {},
"source": [
"MurR"
]
},
{
"cell_type": "code",
"collapsed": false,
"input": [
"catabolism['murR'] = {\n",
" \"transport\": {\n",
" \"carbohydrate\": ['murP'],\n",
" \"amino_acid\": [],\n",
" \"nucleotides\": [],\n",
" \"lipids\": []\n",
" },\n",
" \"recycling\": {\n",
" \"carbohydrate\": ['murQ'],\n",
" \"amino_acid\": [],\n",
" \"lipids\": [],\n",
" \"nucleotides\": []\n",
" },\n",
" \"glycolysis\": [],\n",
" \"TCA\": [],\n",
" \"accessory\": [],\n",
" \"regulators\": {\n",
" \"carbohydrate\": []\n",
" }\n",
" }"
],
"language": "python",
"metadata": {},
"outputs": [],
"prompt_number": 157
},
{
"cell_type": "heading",
"level": 1,
"metadata": {},
"source": [
"NagC"
]
},
{
"cell_type": "code",
"collapsed": false,
"input": [
"catabolism['nagC'] = {\n",
" \"transport\": {\n",
" \"carbohydrate\": ['chbA','chbB','chbC','chiP','crr','galP','manX','manZ','manY'\n",
" 'nagE','nanC','ptsH','ptsI'],\n",
" \"amino_acid\": [],\n",
" \"nucleotides\": [],\n",
" \"lipids\": []\n",
" },\n",
" \"recycling\": {\n",
" \"carbohydrate\": ['chbF','chbG','chbA','chbR','nagA','nagB','nanM'],\n",
" \"amino_acid\": [],\n",
" \"lipids\": [],\n",
" \"nucleotides\": ['nagD']\n",
" },\n",
" \"glycolysis\": [],\n",
" \"TCA\": [],\n",
" \"accessory\": [],\n",
" \"regulators\": {\n",
" \"carbohydrate\": []\n",
" }\n",
" }\n",
"\n",
"\n",
"anabolism['nagC'] = {\n",
" \"macromolecular_synthesis\": [],\n",
" \"biosynthesis\": {\n",
" \"carbohydrate\": ['glmS','glmU'],\n",
" \"nucleotides\": [],\n",
" \"amino_acids\": [],\n",
" \"lipids\": []\n",
" },\n",
" \"accessory\": [],\n",
" \"regulators\": []\n",
" }\n",
"\n",
"\n",
"chemiosmosis['nagC'] = {\n",
" \"ETC\": {\n",
" \"dehydrogenases\": [],\n",
" \"oxidoreductases\": [],\n",
" \"accessory\": []\n",
" },\n",
" \"fermentation\": [],\n",
" \"ion_pumps\": ['feoA','feoB','feoC'],\n",
" \"motility\": [],\n",
" \"regulators\": []\n",
" }\n",
"\n",
"\n",
"unclassified['nagC'] = ['creA','creB','creC','creD','dinI','fimB','ybfN','ydeP']"
],
"language": "python",
"metadata": {},
"outputs": [],
"prompt_number": 158
},
{
"cell_type": "heading",
"level": 1,
"metadata": {},
"source": [
"NanR"
]
},
{
"cell_type": "code",
"collapsed": false,
"input": [
"catabolism['nanR'] = {\n",
" \"transport\": {\n",
" \"carbohydrate\": ['nanT'],\n",
" \"amino_acid\": [],\n",
" \"nucleotides\": [],\n",
" \"lipids\": []\n",
" },\n",
" \"recycling\": {\n",
" \"carbohydrate\": ['nanA','nanE','nanK','nanC','nanM'],\n",
" \"amino_acid\": [],\n",
" \"lipids\": [],\n",
" \"nucleotides\": []\n",
" },\n",
" \"glycolysis\": [],\n",
" \"TCA\": [],\n",
" \"accessory\": [],\n",
" \"regulators\": {\n",
" \"carbohydrate\": []\n",
" }\n",
" }\n",
"\n",
"unclassified['nanR'] = ['fimB','yhcH']"
],
"language": "python",
"metadata": {},
"outputs": [],
"prompt_number": 159
},
{
"cell_type": "heading",
"level": 1,
"metadata": {},
"source": [
"NarP"
]
},
{
"cell_type": "code",
"collapsed": false,
"input": [
"chemiosmosis['narP'] = {\n",
" \"ETC\": {\n",
" \"dehydrogenases\": ['fdhF','fdnG','fdnH','fdnI','hyaA','hyaB','hyaC','hyaD','hyaE','hyaF',\n",
" ],\n",
" \"oxidoreductases\": ['hcr','napA','napB','napC','napG','napH','napD','napF','nirB','nirD',\n",
" 'nirC','nrfA','nrfB','nrfC','nrfD','nrfE','nrfF','nrfG','ydhT','ydhU',\n",
" 'ydhX','ydhW','ydhV','ydhY'],\n",
" \"accessory\": ['ytfE','ccmA','ccmB','ccmC','ccmD','ccmE','ccmF','ccmG','ccmH','cysG',\n",
" 'hcp','norV','norW']\n",
" },\n",
" \"fermentation\": [],\n",
" \"ion_pumps\": [],\n",
" \"motility\": [],\n",
" \"regulators\": []\n",
" }\n",
"\n",
"unclassified['narP'] = ['yeaR','yoaG']"
],
"language": "python",
"metadata": {},
"outputs": [],
"prompt_number": 160
},
{
"cell_type": "heading",
"level": 1,
"metadata": {},
"source": [
"NemR"
]
},
{
"cell_type": "code",
"collapsed": false,
"input": [
"catabolism['nemR'] = {\n",
" \"transport\": {\n",
" \"carbohydrate\": [],\n",
" \"amino_acid\": [],\n",
" \"nucleotides\": [],\n",
" \"lipids\": []\n",
" },\n",
" \"recycling\": {\n",
" \"carbohydrate\": [],\n",
" \"amino_acid\": ['nemA'],\n",
" \"lipids\": [],\n",
" \"nucleotides\": []\n",
" },\n",
" \"glycolysis\": [],\n",
" \"TCA\": [],\n",
" \"accessory\": [],\n",
" \"regulators\": {\n",
" \"carbohydrate\": []\n",
" }\n",
" }"
],
"language": "python",
"metadata": {},
"outputs": [],
"prompt_number": 161
},
{
"cell_type": "heading",
"level": 1,
"metadata": {},
"source": [
"NsrR"
]
},
{
"cell_type": "code",
"collapsed": false,
"input": [
"catabolism['nsrR'] = {\n",
" \"transport\": {\n",
" \"carbohydrate\": [],\n",
" \"amino_acid\": ['putP','ptrA','xasA'],\n",
" \"nucleotides\": [],\n",
" \"lipids\": [],\n",
" \"cofactors\": ['feoA','feoB','tehA','sufA']\n",
" },\n",
" \"recycling\": {\n",
" \"carbohydrate\": ['ydhO','feaB','mhpE','mhpT','yibD','ydbD','yafB','yfcE'],\n",
" \"amino_acid\": ['hflB','tynA','maoC','putA','caiA','caiT','yccA','ydhO'],\n",
" \"lipids\": [],\n",
" \"nucleotides\": ['yieH','cdd','ygiF']\n",
" },\n",
" \"glycolysis\": ['aceE'],\n",
" \"TCA\": [],\n",
" \"accessory\": [],\n",
" \"regulators\": {\n",
" \"carbohydrate\": ['feaR'],\n",
" \"amino_acid\": ['dsdC']\n",
" }\n",
" }\n",
"\n",
"\n",
"anabolism['nsrR'] = {\n",
" \"macromolecular_synthesis\": ['rluB','ftsJ','thrS','clpB','yccK','rpsE','rplR'],\n",
" \"biosynthesis\": {\n",
" \"carbohydrate\": ['folB'],\n",
" \"nucleotides\": ['nrdA','nrdB'],\n",
" \"amino_acids\": [],\n",
" \"lipids\": []\n",
" },\n",
" \"accessory\": [],\n",
" \"regulators\": ['yfhB']\n",
" }\n",
"\n",
"\n",
"chemiosmosis['nsrR'] = {\n",
" \"ETC\": {\n",
" \"dehydrogenases\": ['hycA','hypA','ndh'],\n",
" \"oxidoreductases\": ['hcr'],\n",
" \"accessory\": ['grxD','ytfE','hcp','nrfA','dsbA','hcp','sodB','napF',\n",
" 'yfcF']\n",
" },\n",
" \"fermentation\": [],\n",
" \"ion_pumps\": ['yggT'],\n",
" \"motility\": ['fliA','fliC','fliK','fliL'],\n",
" \"regulators\": ['torS']\n",
" }\n",
"\n",
"\n",
"global_regs['nsrR'] = ['pdhR','lrp']\n",
"unclassified['nsrR'] = ['ygiH','yciQ','mqsR','ygiV','ybeH','yneF','yneG','yihF','yccM','yncL','ydcX',\n",
" 'intZ','yffL','htrG','yigI','yggS','ydfE','intQ','ymcA','ymcB','ydcM','yfhH',\n",
" 'ygbA','mutS','recC','yeeO','smpA','recN','yddW','cbrB']"
],
"language": "python",
"metadata": {},
"outputs": [],
"prompt_number": 162
},
{
"cell_type": "heading",
"level": 1,
"metadata": {},
"source": [
"PaaX"
]
},
{
"cell_type": "code",
"collapsed": false,
"input": [
"catabolism['paaX'] = {\n",
" \"transport\": {\n",
" \"carbohydrate\": [],\n",
" \"amino_acid\": [],\n",
" \"nucleotides\": [],\n",
" \"lipids\": []\n",
" },\n",
" \"recycling\": {\n",
" \"carbohydrate\": ['paaA','paaB','paaC','paaE','paaF','paaG','paaH','paaI','paaJ',\n",
" 'paaK','maoC'],\n",
" \"amino_acid\": [],\n",
" \"lipids\": [],\n",
" \"nucleotides\": []\n",
" },\n",
" \"glycolysis\": [],\n",
" \"TCA\": [],\n",
" \"accessory\": [],\n",
" \"regulators\": {\n",
" \"carbohydrate\": []\n",
" }\n",
" }"
],
"language": "python",
"metadata": {},
"outputs": [],
"prompt_number": 163
},
{
"cell_type": "heading",
"level": 1,
"metadata": {},
"source": [
"PrpR"
]
},
{
"cell_type": "code",
"collapsed": false,
"input": [
"catabolism['prpR'] = {\n",
" \"transport\": {\n",
" \"carbohydrate\": [],\n",
" \"amino_acid\": [],\n",
" \"nucleotides\": [],\n",
" \"lipids\": []\n",
" },\n",
" \"recycling\": {\n",
" \"carbohydrate\": ['prpB','prpC','prpD','prpE'],\n",
" \"amino_acid\": [],\n",
" \"lipids\": [],\n",
" \"nucleotides\": []\n",
" },\n",
" \"glycolysis\": [],\n",
" \"TCA\": [],\n",
" \"accessory\": [],\n",
" \"regulators\": {\n",
" \"carbohydrate\": []\n",
" }\n",
" }"
],
"language": "python",
"metadata": {},
"outputs": [],
"prompt_number": 164
},
{
"cell_type": "heading",
"level": 1,
"metadata": {},
"source": [
"PutA"
]
},
{
"cell_type": "code",
"collapsed": false,
"input": [
"catabolism['putA'] = {\n",
" \"transport\": {\n",
" \"carbohydrate\": [],\n",
" \"amino_acid\": ['putP'],\n",
" \"nucleotides\": [],\n",
" \"lipids\": []\n",
" },\n",
"\n",
" }"
],
"language": "python",
"metadata": {},
"outputs": [],
"prompt_number": 165
},
{
"cell_type": "heading",
"level": 1,
"metadata": {},
"source": [
"RbsR"
]
},
{
"cell_type": "code",
"collapsed": false,
"input": [
"catabolism['rbsR'] = {\n",
" \"transport\": {\n",
" \"carbohydrate\": ['rbsA','rbsB','rbsC'],\n",
" \"amino_acid\": [],\n",
" \"nucleotides\": [],\n",
" \"lipids\": []\n",
" },\n",
" \"recycling\": {\n",
" \"carbohydrate\": ['rbsD','rbsK'],\n",
" \"amino_acid\": [],\n",
" \"lipids\": [],\n",
" \"nucleotides\": []\n",
" },\n",
"\n",
" }"
],
"language": "python",
"metadata": {},
"outputs": [],
"prompt_number": 166
},
{
"cell_type": "heading",
"level": 1,
"metadata": {},
"source": [
"RhaS"
]
},
{
"cell_type": "code",
"collapsed": false,
"input": [
"catabolism['rhaS'] = {\n",
" \"transport\": {\n",
" \"carbohydrate\": ['rhaT'],\n",
" \"amino_acid\": [],\n",
" \"nucleotides\": [],\n",
" \"lipids\": []\n",
" },\n",
" \"recycling\": {\n",
" \"carbohydrate\": ['rhaA','rhaB','rhaD'],\n",
" \"amino_acid\": [],\n",
" \"lipids\": [],\n",
" \"nucleotides\": []\n",
" },\n",
" \"glycolysis\": [],\n",
" \"TCA\": [],\n",
" \"accessory\": [],\n",
" \"regulators\": {\n",
" \"carbohydrate\": []\n",
" }\n",
" }"
],
"language": "python",
"metadata": {},
"outputs": [],
"prompt_number": 167
},
{
"cell_type": "heading",
"level": 1,
"metadata": {},
"source": [
"TreR"
]
},
{
"cell_type": "code",
"collapsed": false,
"input": [
"catabolism['treR'] = {\n",
" \"transport\": {\n",
" \"carbohydrate\": ['treB'],\n",
" \"amino_acid\": [],\n",
" \"nucleotides\": [],\n",
" \"lipids\": []\n",
" },\n",
" \"recycling\": {\n",
" \"carbohydrate\": ['treC'],\n",
" \"amino_acid\": [],\n",
" \"lipids\": [],\n",
" \"nucleotides\": []\n",
" },\n",
" \"glycolysis\": [],\n",
" \"TCA\": [],\n",
" \"accessory\": [],\n",
" \"regulators\": {\n",
" \"carbohydrate\": []\n",
" }\n",
" }"
],
"language": "python",
"metadata": {},
"outputs": [],
"prompt_number": 168
},
{
"cell_type": "heading",
"level": 1,
"metadata": {},
"source": [
"TyrR"
]
},
{
"cell_type": "code",
"collapsed": false,
"input": [
"catabolism['tyrR'] = {\n",
" \"transport\": {\n",
" \"carbohydrate\": [],\n",
" \"amino_acid\": ['aroP','mtr','tyrP'],\n",
" \"nucleotides\": [],\n",
" \"lipids\": []\n",
" },\n",
" \"recycling\": {\n",
" \"carbohydrate\": [],\n",
" \"amino_acid\": [],\n",
" \"lipids\": [],\n",
" \"nucleotides\": []\n",
" },\n",
" \"glycolysis\": [],\n",
" \"TCA\": [],\n",
" \"accessory\": [],\n",
" \"regulators\": {\n",
" \"carbohydrate\": []\n",
" }\n",
" }\n",
"\n",
"\n",
"anabolism['tyrR'] = {\n",
" \"macromolecular_synthesis\": [],\n",
" \"biosynthesis\": {\n",
" \"carbohydrate\": [],\n",
" \"nucleotides\": [],\n",
" \"amino_acids\": ['aroF','aroG','aroL','aroM','folA','tyrA','tyrB'],\n",
" \"lipids\": []\n",
" },\n",
" \"accessory\": [],\n",
" \"regulators\": []\n",
" }\n",
"\n",
"\n",
"unclassified['tyrR'] = ['yaiA']"
],
"language": "python",
"metadata": {},
"outputs": [],
"prompt_number": 169
},
{
"cell_type": "heading",
"level": 1,
"metadata": {},
"source": [
"UlaR"
]
},
{
"cell_type": "code",
"collapsed": false,
"input": [
"catabolism['ulaR'] = {\n",
" \"transport\": {\n",
" \"carbohydrate\": ['ulaA','ulaB','ulaC'],\n",
" \"amino_acid\": [],\n",
" \"nucleotides\": [],\n",
" \"lipids\": []\n",
" },\n",
" \"recycling\": {\n",
" \"carbohydrate\": ['ulaD','ulaE','ulaF'],\n",
" \"amino_acid\": [],\n",
" \"lipids\": [],\n",
" \"nucleotides\": []\n",
" },\n",
" \"glycolysis\": [],\n",
" \"TCA\": [],\n",
" \"accessory\": [],\n",
" \"regulators\": {\n",
" \"carbohydrate\": []\n",
" }\n",
" }\n"
],
"language": "python",
"metadata": {},
"outputs": [],
"prompt_number": 170
},
{
"cell_type": "heading",
"level": 1,
"metadata": {},
"source": [
"UxuR"
]
},
{
"cell_type": "code",
"collapsed": false,
"input": [
"catabolism['uxuR'] = {\n",
" \"transport\": {\n",
" \"carbohydrate\": ['gntP','uidB','uidC'],\n",
" \"amino_acid\": [],\n",
" \"nucleotides\": [],\n",
" \"lipids\": []\n",
" },\n",
" \"recycling\": {\n",
" \"carbohydrate\": ['uxuA','uxuB'],\n",
" \"amino_acid\": [],\n",
" \"lipids\": [],\n",
" \"nucleotides\": []\n",
" },\n",
" \"glycolysis\": [],\n",
" \"TCA\": [],\n",
" \"accessory\": [],\n",
" \"regulators\": {\n",
" \"carbohydrate\": []\n",
" }\n",
" }"
],
"language": "python",
"metadata": {},
"outputs": [],
"prompt_number": 171
},
{
"cell_type": "heading",
"level": 1,
"metadata": {},
"source": [
"XapR"
]
},
{
"cell_type": "code",
"collapsed": false,
"input": [
"catabolism['xapR'] = {\n",
" \"transport\": {\n",
" \"carbohydrate\": ['xapB'],\n",
" \"amino_acid\": [],\n",
" \"nucleotides\": [],\n",
" \"lipids\": []\n",
" },\n",
" \"recycling\": {\n",
" \"carbohydrate\": ['xapA'],\n",
" \"amino_acid\": [],\n",
" \"lipids\": [],\n",
" \"nucleotides\": []\n",
" },\n",
" \"glycolysis\": [],\n",
" \"TCA\": [],\n",
" \"accessory\": [],\n",
" \"regulators\": {\n",
" \"carbohydrate\": []\n",
" }\n",
" }"
],
"language": "python",
"metadata": {},
"outputs": [],
"prompt_number": 172
},
{
"cell_type": "heading",
"level": 1,
"metadata": {},
"source": [
"XylR"
]
},
{
"cell_type": "code",
"collapsed": false,
"input": [
"catabolism['xylR'] = {\n",
" \"transport\": {\n",
" \"carbohydrate\": ['xylF','xylG','xylH'],\n",
" \"amino_acid\": [],\n",
" \"nucleotides\": [],\n",
" \"lipids\": []\n",
" },\n",
" \"recycling\": {\n",
" \"carbohydrate\": ['xylA','xylB'],\n",
" \"amino_acid\": [],\n",
" \"lipids\": [],\n",
" \"nucleotides\": []\n",
" },\n",
" \"glycolysis\": [],\n",
" \"TCA\": [],\n",
" \"accessory\": [],\n",
" \"regulators\": {\n",
" \"carbohydrate\": []\n",
" }\n",
" }"
],
"language": "python",
"metadata": {},
"outputs": [],
"prompt_number": 173
},
{
"cell_type": "code",
"collapsed": false,
"input": [],
"language": "python",
"metadata": {},
"outputs": [],
"prompt_number": 173
},
{
"cell_type": "code",
"collapsed": false,
"input": [],
"language": "python",
"metadata": {},
"outputs": [],
"prompt_number": 173
},
{
"cell_type": "code",
"collapsed": false,
"input": [],
"language": "python",
"metadata": {},
"outputs": [],
"prompt_number": 173
},
{
"cell_type": "code",
"collapsed": false,
"input": [],
"language": "python",
"metadata": {},
"outputs": []
}
],
"metadata": {}
}
]
}
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