GPML-Rhea

Collect chemical reactions from a GPML file and look for matching Rhea equations.

Pathway requirements:

• MIM interactions compatible with https://github.com/BiGCAT-UM/WikiPathwaysInteractions/tree/master/FilesGPML#readme
• Metabolites with ChEBI identifiers

Install

System requirements:

• Node.js v14
• npm (usually comes with Node.js)

Installing Node.js on Linux

sudo apt-get install nodejs-dev node-gyp libssl1.0-dev
sudo apt install npm

Installing GPML-Rhea

npm install --global @larsgw/gpml-rhea

Alternatively, run "without" installing:

npx @larsgw/gpml-rhea [options]

Usage

GPML-Rhea

  gpml-rhea [file]             Read file
  gpml-rhea -                  Read from standard in
  gpml-rhea -v, --version      Get the version
  gpml-rhea -h, --help         Print this message

Example

> curl -L -o pathway.gpml https://webservice.wikipathways.org/getPathwayAs?fileType=gpml&pwId=WP5019&revision=113587
> gpml-rhea pathway.gpml
id192c7b4a: 5,10-Methenyltetrahydrofolate + NADH → 5,10-Methylenetetrahydrofolate + NAD(1-)
---------------------------------------------
Rhea: 0 results
---------------------------------------------

id4f3af248: Oxidised ferredoxin → Reduced ferredoxin
---------------------------------------------
Rhea: 0 results
---------------------------------------------

id59fbd0e3: 10-Formyltetrahydrofolate + dihydrogen → 5,10-Methenyltetrahydrofolate
---------------------------------------------
Rhea: 0 results
---------------------------------------------

id8e976caf: 5-Methyltetrahydrofolate → methyl + Tetrahydrofolate
---------------------------------------------
Rhea: 0 results
---------------------------------------------

idb70e2922: NAD(1-) → NADH
---------------------------------------------
Rhea: 0 results
---------------------------------------------

idcb0cc195: formate + ATP + Tetrahydrofolate → 10-Formyltetrahydrofolate + hydrogenphosphate + ADP
---------------------------------------------
Rhea: 0 results
---------------------------------------------

ide2e37f0: 5,10-Methylenetetrahydrofolate + NADH → 5-Methyltetrahydrofolate + NAD(1-)
---------------------------------------------
Rhea: 0 results
---------------------------------------------

ideb932d04: carbon monooxide + HSCoA + methyl → acetyl-CoA
---------------------------------------------
Rhea: 0 results
---------------------------------------------

idee9950c3: carbon dioxide + dihydrogen → formate + hydron
---------------------------------------------
Rhea: 1 results
    27610: formate + H(+) = CO2 + H2
---------------------------------------------

idf6f6d75: dihydrogen → hydron
---------------------------------------------
Rhea: 13 results
    24636: H2 + NAD(+) = H(+) + NADH
    27610: formate + H(+) = CO2 + H2
    29047: a menaquinone + 2 H(+)(in) + H2 = a menaquinol + 2 H(+)(out)
    29051: 2 H(+)(in) + H2 + menaquinone-8 = 2 H(+)(out) + menaquinol-8
    29055: a ubiquinone + 2 H(+)(in) + H2 = a ubiquinol + 2 H(+)(out)
    29059: 2 H(+)(in) + H2 + ubiquinone-8 = 2 H(+)(out) + ubiquinol-8
    30279: 2 H2 + NAD(+) + 2 oxidized [2Fe-2S]-[ferredoxin] = 3 H(+) + NADH + 2 reduced [2Fe-2S]-[ferredoxin]
    35591: H2 + n sulfur = H(+) + hydrogen sulfide + (n-1) sulfur
    17445: H2 + 2 oxidized [2Fe-2S]-[ferredoxin] = 2 H(+) + 2 reduced [2Fe-2S]-[ferredoxin]
    18637: H2 + NADP(+) = H(+) + NADPH
    20017: 5,10-methenyl-5,6,7,8-tetrahydromethanopterin + H2 = 5,10-methylenetetrahydromethanopterin + H(+)
    20625: 2 [Fe(III)-cytochrome c3] + H2 = 2 [Fe(II)-cytochrome c3] + 2 H(+)
    55748: coenzyme B + coenzyme M + 2 H(+) + 2 reduced [2Fe-2S]-[ferredoxin] = coenzyme M-coenzyme B heterodisulfide + 2 H2 + 2 oxidized [2Fe-2S]-[ferredoxin]
---------------------------------------------