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added filter by compound
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@Robaina
Robaina committed Aug 17, 2022
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145 changes: 108 additions & 37 deletions README.ipynb
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"This is an ongoing project!"
]
},
{
"cell_type": "markdown",
"metadata": {},
"source": [
"## Installation\n",
"1. ```pip install brendapyrser```\n",
"\n",
"or\n",
"\n",
"2. Git clone project to local directory.\n",
"\n",
" In terminal navigate to directory and enter: ```python setup.py install```"
]
},
{
"cell_type": "code",
"execution_count": 6,
"execution_count": 1,
"metadata": {},
"outputs": [],
"source": [
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},
{
"cell_type": "code",
"execution_count": 7,
"execution_count": 2,
"metadata": {},
"outputs": [
{
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" "
],
"text/plain": [
"<brendapyrser.parser.BRENDA at 0x7f2880f2d130>"
"<brendapyrser.parser.BRENDA at 0x7fe79c7db760>"
]
},
"execution_count": 7,
"execution_count": 2,
"metadata": {},
"output_type": "execute_result"
}
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},
{
"cell_type": "code",
"execution_count": 9,
"execution_count": 3,
"metadata": {},
"outputs": [
{
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" "
],
"text/plain": [
"<brendapyrser.parser.Reaction at 0x7f2311f0c8e0>"
"<brendapyrser.parser.Reaction at 0x7fead617e820>"
]
},
"execution_count": 9,
"execution_count": 3,
"metadata": {},
"output_type": "execute_result"
}
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"plt.show()"
]
},
{
"cell_type": "code",
"execution_count": 12,
"metadata": {},
"outputs": [
{
"data": {
"text/plain": [
"[{'substrates': ['AKT1S1', 'ATP'], 'products': ['ADP', 'phospho-AKT1S1']},\n",
" {'substrates': ['TDP', 'phosphoenolpyruvate'],\n",
" 'products': ['TTP', 'pyruvate | 95% yield |']},\n",
" {'substrates': ['ATP', 'pyruvate'],\n",
" 'products': ['ADP', 'phosphoenolpyruvate']},\n",
" {'substrates': ['ADP', 'phosphoenolpyruvate'],\n",
" 'products': ['ATP', 'pyruvate']},\n",
" {'substrates': ['ATP', 'prothymosin alpha'],\n",
" 'products': ['ADP', 'phospho-prothymosin alpha']}]"
]
},
"execution_count": 12,
"metadata": {},
"output_type": "execute_result"
}
],
"source": [
"r.substratesAndProducts "
]
},
{
"cell_type": "markdown",
"metadata": {},
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"source": [
"That's interesting! typical NADH concentrations are low in _Escherichia coli_, e.g., from [BioNumbers](http://book.bionumbers.org/what-are-the-concentrations-of-free-metabolites-in-cells/) we get a value of 0.083 mM. The median KM value for NADH among all enzymes binding it is lower as we see in the plot above! Hence, it looks like most enzymes are (nearly) saturated for NADH and thus fluxes are sort of independent of NADH concentration."
]
},
{
"cell_type": "markdown",
"metadata": {},
"source": [
"# 4 Filtering reactions by specific compound\n",
"\n",
"We can also filter reactions in BRENDA by a specific compound: substrate, product or either of the two. Let's filter reactions containg _geraniol_ as a substrate, product or both to exemplify this feature"
]
},
{
"cell_type": "code",
"execution_count": 25,
"metadata": {},
"outputs": [
{
"data": {
"text/html": [
"\n",
" <table>\n",
" <tr>\n",
" <td><strong>Enzyme identifier</strong></td><td>2.5.1.19</td>\n",
" </tr><tr>\n",
" <td><strong>Name</strong></td><td>3-phosphoshikimate 1-carboxyvinyltransferase</td>\n",
" </tr><tr>\n",
" <td><strong>Systematic name</strong></td><td>phosphoenolpyruvate:3-phosphoshikimate 5-O-(1-carboxyvinyl)-transferase</td>\n",
" </tr><tr>\n",
" <td><strong>Reaction type</strong></td><td>Enolpyruvate group transfer (#3,52,55# induced-fit mechanism, formation</td>\n",
" </tr><tr>\n",
" <td><strong>Reaction</strong></td><td>phosphoenolpyruvate + 3-phosphoshikimate <=> phosphate +5-O-</td>\n",
" </tr>\n",
" </table>\n",
" "
],
"text/plain": [
"<brendapyrser.parser.Reaction at 0x7fe7502c1280>"
]
},
"execution_count": 25,
"metadata": {},
"output_type": "execute_result"
}
],
"source": [
"substrate_rxns = brenda.reactions.filter_by_substrate(\"phosphoenolpyruvate\")\n",
"substrate_rxns[2]"
]
},
{
"cell_type": "code",
"execution_count": 26,
"metadata": {},
"outputs": [
{
"data": {
"text/html": [
"\n",
" <table>\n",
" <tr>\n",
" <td><strong>Enzyme identifier</strong></td><td>2.5.1.7</td>\n",
" </tr><tr>\n",
" <td><strong>Name</strong></td><td>Udp-n-acetylglucosamine 1-carboxyvinyltransferase</td>\n",
" </tr><tr>\n",
" <td><strong>Systematic name</strong></td><td>phosphoenolpyruvate:UDP-N-acetyl-D-glucosamine</td>\n",
" </tr><tr>\n",
" <td><strong>Reaction type</strong></td><td>Carboxyvinyl group transfer</td>\n",
" </tr><tr>\n",
" <td><strong>Reaction</strong></td><td>phosphoenolpyruvate + UDP-N-acetyl-alpha-D-glucosamine <=> phosphate +UDP-N-acetyl-3-O-</td>\n",
" </tr>\n",
" </table>\n",
" "
],
"text/plain": [
"<brendapyrser.parser.Reaction at 0x7fe7502c1d00>"
]
},
"execution_count": 26,
"metadata": {},
"output_type": "execute_result"
}
],
"source": [
"compound_rxns = brenda.reactions.filter_by_compound(\"phosphoenolpyruvate\")\n",
"compound_rxns[7]"
]
}
],
"metadata": {
"interpreter": {
"hash": "367a058ebb24ea2c2bb1633bf810ec6a1a05f59e065f27f721ea93103e797079"
},
"kernelspec": {
"display_name": "Metabolism",
"display_name": "Python 3 (ipykernel)",
"language": "python",
"name": "python3"
},
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"name": "python",
"nbconvert_exporter": "python",
"pygments_lexer": "ipython3",
"version": "3.9.6"
"version": "3.8.12"
}
},
"nbformat": 4,
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