Help on curation of STAD_ORYSA

[Tanya Berardini]

Pankaj,


On Fri, 14 Jun 2002, Pankaj Jaiswal wrote:

> I am confused on how to curate a rice entry which has a similarity to
> Arabidopsis protein
> http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=search&db=nucleotide&doptcmdl=genbank&term=%22AF395441%22
>
> Which biological process should I include for
> activator signal for Jasmonic acid dependent defence response
>
> In Arabidopsis, the enzyme catalyzes a desaturation step that is required for
> Jasmonic acid biosynthesis. Also acts as an activator signal for Jasmonic acid
> dependent defence response at the time of pathogen interaction

> Annotation for rice entry
> http://www.gramene.org/perl/protein_search?protein_id=78051
>
> I have discarded the electronic annotation from Interpro matches.
>
> Molecular Function|acyl-[acyl-carrier-protein]
> desaturase|GO:0045300|GR_REF:62|ISS
> Biological Process|fatty acid elongation, unsaturated fatty
> acid|GO:0019368|GR_REF:62|ISS
> Cellular Component|plastid stroma|GO:0009532|GR_REF:62|ISS
> Cellular Component|chloroplast stroma|GO:0009570|GR_REF:62|ISS

The ISS annotations relating to the desaturase activity for function,
location, and biological process are fine. I would _not_ annotate to a
very specific biological process for the defense response related terms as
these are functions that have been described in Arabidopsis not rice.

The information below might help you in future annotations:

>From the GO documentation page:

http://www.geneontology.org/doc/GO.evidence.html

ISS inferred from sequence or structural similarity
        Sequence similarity (homologue of/most closely related to)
        Recognized domains
        Structural similarity
        Southern blotting
    Comment: Use this code for BLAST (or other sequence similarity
detection method) results that have been reviewed for accuracy by a
curator. If the result has not been reviewed, use IEA. ISS can also be
used for sequence similarities reported in published papers, if the
curator thinks the result is reliable enough.

**When the gene is a "homologue of," can infer fairly detailed function
and location (cellular component) but err on the side of low resolution
for processes.

For recognized domains, attribution to any of the ontologies will probably
be at low resolution.

    We recommend making an entry in the "with" column when using this
evidence code (i.e. include an identifier for the similar sequence).


> Also we need to add GO terms
> Fatty acid desaurase
> and
> add "stearoyl ACP desaturase" as synonym for acyl-[acyl-carrier-protein]
> desaturase; GO:0045300


fatty acid desaturase is in the GO as a synonym for stearoyl-CoA
desaturase GO:0004768, they share the same EC number 1.14.19.1
(was EC 1.14.99.5)

I looked up EC 1.14.19.2 and the synonyms for acyl-[acyl-carrier proteii]
desaturase that I found were: stearyl acyl carrier protein desaturase and
stearyl-ACP desaturase.  These can be added without any problem.

Hope this helps,

Tanya


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Tanya Berardini, Ph.D.			tberardi at acoma.stanford.edu
The Arabidopsis Information Resource	FAX: (650) 325-6857
Carnegie Institution of Washington	Tel: (650) 325-1521 ext. 325
Department of Plant Biology		URL: http://arabidopsis.org/
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