Help!: About proteins

puigdomenech at puigdomenech at
Thu Feb 17 18:50:24 EST 1994

Could someone help me?

I have cloned a maize gene which is being sequenced. I have only
six hundred base pairs of sequence divided in two parts (the two
endpoints of an insert). Using GCG I have run a FASTA using the
nucleotide and the translated ORF, but I could not find any
significant homology. I have run also a scan looking for
signatures or motifs along my clone. The only site the GCG could
find was an "ATP/GTP binding site". Do you know how predictive
are the findings GCG make? Could I say that my clone has an
ATP/GTP binding site? With which degree of probability? May be
90%?, 50%?, 10%?, 0.0001%?...
I ran also an old release (1989) of PCGENE, which could find the
same motif and some Casein kinase II and Protein kinase C
phosphorylation sites too. I also ran the PESTFIND program, which
belongs to PCGENE, and it could detect a "good" PEST sequence
(that means a score over 5). What does it REALLY mean?

I know that my english is worse than it should be. I beg your

            Enrique Graziano-Areste
             (egagmp at

Centro de Investigaci¢n y desarrollo.
Consejo Superior de Investigaciones Cient¡ficas.
C/Jordi Girona Salgado 18-26
08034 Barcelona

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