Download week3bioinformatics

John Reiser
3/29/11
Bioinformatics: Week 3
Blast at NCBI
1) PPT1 FASTA File:
>gi|4506031|ref|NP_000301.1| palmitoyl-protein thioesterase 1 isoform 1 precursor [Homo sapiens]
MASPGCLWLLAVALLPWTCASRALQHLDPPAPLPLVIWHGMGDSCCNPLSMGAIKKMVE
KKIPGIYVLSLEIGKTLMEDVENSFFLNVNSQVTTVCQALAKDPKLQQGYNAMGFSQGGQ
FLRAVAQRCPSPPMINLISVGGQHQGVFGLPRCPGESSHICDFIRKTLNAGAYSKVVQERLV
QAEYWHDPIKEDVYRNHSIFLADINQERGINESYKKNLMALKKFVMVKFLNDSIVDPVDS
EWFGFYRSGQAKETIPLQETSLYTQDRLGLKEMDNAGQLVFLATEGDHLQLSEEWFYAHII
PFLG
2) Homologs for the PPT1 (palmitoyl-protein thioesterase 1 isoform 1) protein date back all the
way to eukaryotic organisms of the fungi/metazoa family. The first known organism with a
conserved domain in this sequence is Naegleria ruberi. This is the initial lineage where hits are
seen for this protein. There are 171 hits in 63 organisms dating back to the evolutionary beginning
of eukaryotic cells. This means that this gene must be highly conserved and highly important in all
organisms.
3) Amino acids 42, 47, 48, 116, 123, 124, 125, 130, 153, 243, 248, 251, 254, and 280 are single,
fully conserved amino acids within 15 model organisms (all mammals). The cynomolgous monkey
has an identical amino acid sequence for the PPT1 protein as humans. This is evidence that this
gene is highly conserved. The conserved domains are amino acids that are most likely imperative
to the function of the PPT1 enzyme in its catabolism of lipid-modified proteins in the lysosome. A
point mutation in the DNA sequence that substitutes a different amino acid at any of the conserved
domains could be the cause of a dysfunctional protein.
Biology Workbench
1) Boxshade
2)
3)