Actually, the input file is ... [update: quoted from this post]

Rather than saying (update: in a different post!) what your example data actually is, why not post that data as it actually is, in a form immediately usable by other monks (who are trying to help you). That is, use <code> ... </code> tags to post your data, maybe something like:

<code>
>sp_0005_SySynthetic ConstructTumor protein p53 N-terminal transcripti
+on-activation domain
VQLQESGGGLVQAGGSLRLSCAASGRAVSMYNMGWFRQAPGQERELVAAISRGGSIYYA
DSVKGRFTISRDNAKNTLYLQMNNLKPEDTGVYQCRQGSTLGQGTQVTVSS

>sp_0017_CaCamelidSorghum bicolor multidrug and toxic compound extrusi
+on sbmate
HVQLVESGGGSVQAGGSLRLTCAASGFTFSNYYMSWVRQAPGKGLEWVSSIYSVGSNGYY
ADSVKGRSTISRDNAKNTLYLQMNSLKPEDTAVYYCAAEPGGSWWDAYSYWGQGTQVTVS
S
</code>
[download]

In addition to being your exact example data, this data is easily [download]-able by anyone who might want to help with this problem. You might want to add this <code>-tagged example data as an update (see How do I change/delete my post?) to your original post in addition to finally updating this post, or at the very least update this post and add to the OP a note saying that example data can be found there.

Please see Markup in the Monastery, Writeup Formatting Tips and What shortcuts can I use for linking to other information?, and perhaps some of the articles in the Understanding and Using PerlMonks section of the Monastery's Tutorials.

Update: Some trivial wording changes; added links to actual "Actually..." post.