Question: Retrieve all reactions for a given kegg pathway
0
gravatar for neha 114
3.1 years ago by
neha 1140
United States
neha 1140 wrote:

Hello, I am trying to derive all the reactions specific for a kegg pathway. For example " for metabolic pathway" from ehi :ehi01100 , I want to extract all the reactions involved with its specific reaction equation entry.

I have followed this question already asked, but unable to derive the results for my case. Kindly help please. Your help is greatly appreciated.

Thanks in advance.

kegg • 2.2k views
ADD COMMENTlink modified 3.1 years ago by Damian Kao15k • written 3.1 years ago by neha 1140
1
gravatar for natasha.sernova
3.1 years ago by
natasha.sernova3.5k
natasha.sernova3.5k wrote:

This is KEGG general site.

http://www.genome.jp/kegg/kegg1d.html

But I think it's better to start from this site below:

KEGG-tutorial:

http://genome.jgi.doe.gov/Tutorial/tutorial/kegg.html

Using the KEGG browser, you can:

view enzymes related to a pathway.

view predicted genes related to a pathway.

view maps of reference pathways.

browse through KEGG pathways.

search KEGG.

compare models to KEGG assignments in related organisms.

The tutorial has "clickable" words or even sentences, and the click will lead you to what you have chosen.

There is a paper describing pathways in KEGG:

http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3150042/

It answers your question to some extent, doesn't it?

I hope it may help.

<h6>#</h6>

There is another way to get all pathways for any organism.

Go here:

http://www.genome.jp/kegg/pathway.html

Select organism – press on ‘organism’ , enter your organism 4-letter name near

‘Find three- or four-letter KEGG organism code’ , press ‘select’ and ‘GO’.

After that you will have all pathways KEGG has for the organism.

‘map’ to the left of the ‘organism’ will be replace with its name.

http://www.kegg.jp/kegg-bin/search_pathway_text?map=ehi&keyword=&mode=1&viewImage=true

with all pathways KEGG found for it.

You can even generate possible reaction paths:

http://www.genome.jp/tools/pathcomp/

From here

http://www.genome.jp/dbget-bin/www_bget?ehi:EHI_007460+ehi:EHI_040600+ehi:EHI_088080+ehi:EHI_118110+ehi:EHI_193190

I selected ' Pathways 2' from the links on the left panel:

ID Definition

ehi00600 Sphingolipid metabolism - Entamoeba histolytica ehi01100 Metabolic pathways - Entamoeba histolytica

http://www.genome.jp/kegg-bin/show_pathway?ehi00600

http://www.genome.jp/kegg-bin/show_pathway?ehi01100

<h6>#</h6>

Start again - back to your question:

Retrieve all reactions for a given kegg pathway

1) Start here

http://genome.jgi.doe.gov/Tutorial/tutorial/kegg.html

Choose in the table

KEGG metabolic pathways

or

KEGG regulatory pathways

OR

KEGG Metabolic Pathways -

go to the line 'browse through KEGG pathways'.

2) Do go to the Table: JGI Genome portal tutorial, Other functions below and click on the pathways you needed – regulatory or metabolic ones

I have not seen the way you need: Find a pathway then Retrieve all the reactions

I think you can go only in the opposite direction:

Retrieve the full list of all the reactions as I described above, then find a pathway or pathways you need among them

Good luck!

ADD COMMENTlink modified 3.1 years ago • written 3.1 years ago by natasha.sernova3.5k
1
gravatar for Damian Kao
3.1 years ago by
Damian Kao15k
USA
Damian Kao15k wrote:

KEGG has a useful REST API for retrieval database links. For example, you can get all reactions by pathway like this:

http://rest.kegg.jp/link/reaction/map00010

switch out map00010 by the pathway ID you want.

ADD COMMENTlink written 3.1 years ago by Damian Kao15k

That seems to work fine for default pathways but does not work for species specific pathways. Do you have a solution for that, too? So e.g. how to get all reactions of E.coli present in map00010?

ADD REPLYlink written 2.7 years ago by cleb60
0
gravatar for neha 114
3.1 years ago by
neha 1140
United States
neha 1140 wrote:

Thank you very much. It helped me a lot.

ADD COMMENTlink written 3.1 years ago by neha 1140

You should use the "Upvote" botton to translate your gratitude into "points" for @Natasha. The "check" mark button on @natasha's answer can also be used to signify that you "accept" it as a valid/good answer.

ADD REPLYlink written 3.1 years ago by genomax68k
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