I annotated the Aspergillus proteins by Kaas server and Kegg however, I am not confirmed whether the pathway annotation is correct. For example protein XP_752857.1 (AFUA_1G14880) is annotated with K01426 kegg orthology number (http://www.genome.jp/dbget-bin/www_bget?afm:AFUA_1G14880). The entry shows 3 pathways here. However if I click on K01426 then it shows 5 more pathways. So, what could I expect with this associated EC number 3.5.1.4? It involve in 3 pathways or 8 pathways?
Another example - for protein XP_753224.1 (AFUA_1G14330) no pathway were annotated (http://www.genome.jp/dbget-bin/www_bget?afm:AFUA_1G14330) but the kaas server assigned it kegg orthology number K00224 which shows 3 pathways (http://www.genome.jp/dbget-bin/www_bget?ko:K00224).
Could someone please explain me both the situations and best way to annotate metabolic pathways.
@Arafat- Dear, as per my experience STRING database is much specific for protein-protein interactions.
from my experience, best is to go for ingenuity pathway analysis
http://www.ingenuity.com/products/ipa
you can also have a free trial
@Ashmit- I think that will give you some sort of insight in every steps.
AFUA_1G14800 in Aspergillus fumigatus is annotated with KO1426, KO1426 also include other annotated pathways from other species because of its associated orthologs. It's similar to AFUA_1G14330.
1.When you go to the link you mentioned (http://www.genome.jp/dbget-bin/www_bget?afm:AFUA_1G14880), shows you three pathways, these are the actual pathways which is used by organism. Kegg is a database which will have a list of pathways associated with particular EC number, but which pathways are carried in your organism or organism of interest is you have check in the drop down list kegg provides, when you open a specific pathway. For instance if you check ko00627 and find out whether your organism involves this pathway or not, you wont find it.
2. Answer to the second question is even same, open the pathway check in drop down list for your organism whether it is present or not.
Try to get annotations from annotation servers along with KAAS and kegg. This would help you to have a better annotations. Try to find out if this organism have a metabolic model if so than you can take annotations from there. You can try other methods of sequence comparison like reverse-blast, checking in Pfam database. Through literature even you can get annotation help as they will mention about specific reactions and enzymes involved.
I hope it helps you little.
Thanks to all. It seems the ko pathway matches are not the real matches for the query organism. It may be only a hit to the ortholog protein present in the metabolic pathway of other organisms.
Try DAVID (http://david.abcc.ncifcrf.gov/), there are lots of organisms annotated
Just a remark, which may or may not be part of your problem. Enzymes perform reactions that are annotated with EC numbers and thus enzymes can indeed have associated EC numbers. Not every reaction with a specific EC number will be catalysed by every enzyme able to perform that reaction, for instance because the enzyme is not present at the location where its substrate appears. That is especially true in more complex organisms. So you might find more pathways for the EC number than for the enzyme itself and that is not necessarily wrong.
An other remark, it exist a database of predicted metabolic pathways for fungi : fungipath (www.fungipath.u-psud.fr/). This web site allow you to analyse the distribution of presence/absence of enzyme activities in function of organisms or taxonomic groups. If you want, you can also compare your sequences with the sequences present in the database.
www.fungipath.u-psud.fr/
#Pereira Thanks. I searched the database but there is something fishy. 1. If I compared A. fumigatus and A. nidulans it shows only 18 result(s) which is not true. 2. For exporting the pathway of a single organism, no option is given to export all pathways of that organism.
Thanks all for your useful comments. If I correctly understand for the organism Kegg have annotated pathway we can retrieve directly from there. For example for A. nidulans the Kegg pathway map shows around 100 pathways (http://www.genome.jp/kegg-bin/show_organism?menu_type=pathway_maps&org=ani), it means only these full pathway are present in A. nidulans that does not include "Z" pathway . So, if we get "Z" pathway hit by kaas/david/etc for the A. nidulans proteins than that hits may be the part of other organism pathway (and hits are solely based on orthology) but some of such hits does not represent the presence of " Z" pathway in A. nidulans. Please correct me if I am wrong.
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