Graded HW 5-2
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Name: Danyael Murphy
Modules 09-11: Graded Homework 5
1. (0.6) Use prosite (
http://prosite.expasy.org/
) to find motifs in CAA22878
. Unclick the checkbox that would exclude patterns that match frequently. Scan Prosite.
a. (0.2) How many distinct patterns are
above the line that reads “hits by patterns with a high probability of occurrence or by user-defined patterns?”
1
b. (0.2) Looking at the pattern that is above that line, what types of molecules do proteins with this pattern
transport?
Sugar/carbohydrates
c. (0.2) Click on the prosite number (starts with PS). Scroll down for the consensus pattern. At what position in the pattern is an "any amino acid except threonine (T) or aspartic acid (D)?"
7
th
position
2. (0.6) Analyze the following sequence:
>hypothetical protein [Comamonadaceae bacterium CR]
MSLKERIQEEMKAAMRAKDTARLGAIRLLLAAIKQKEVDERVMLDDAAIIAVVDKLIKQRRDSVTAYQQA
QRSDLADKEAAEITVLEAYLPQRWSRAEVEEAVSRVVAETAATGPGDMGKVMAAVKAQCQGKADMAVVSQ
VVKAALAARGG
Using the Lehninger scale, what is the charge of this protein at pH 4.0, pH 7.0, and
pH 9.0? Refer to the attached document for the syntax of calculating charge in the R Peptides package.
pH
charge
4.0
12.79
7.0
1.96
9.0
0.46
3. (0.8) Use the protein below for transmembrane prediction:
> Dpy19/1 protein [Mus musculus]
MVTRGFLEFQLFGWLFGKVHPGAVVFAILAAMSIQGSANLQTQWNIVGEFSNLPQEELIEWIRYSTKPDA
VFAGAMPTMASVKLSALRPVVNHPHYEDAGLRARTKIVYSMYSRKAPEDVKKELMKLKVNYYILEESWCI
RRSKPGCSMPEIWDVEDPDNAGKTPLCNILVKDSKPHFTTVFQNSVYKVLEVLRQ
Run Phobius
and TMHMM
on this protein. Compare and contrast the results. What
are the exact predicted transmembrane locations and approximate probabilities from the graph?
Transmembrane location
Approximate probability of TM
Phobius
12…34
90%
TMHMM
1…41
100%
4. Use this mitochondrial protein from yeast.
>yeast mitochondrial protein
MVLLHKSTHIFPTDFASVSRAFFNRYPNPYSPHVLSIDTISRNVDQEGNLRTTRLLKKSGKLPTWVKPFL
RGITETWIIEVSVVNPANSTMKTYTRNLDHTGIMKVEEYTTYQFDSATSSTIADSRVKFSSGFNMGIKSK
VEDWSRTKFDENVKKSRMGMAFVIQKLEEARNPQF
Try the following localization programs. List the organelle prediction (if any), and probability (if any).
a. (0.2) TargetP (
https://services.healthtech.dtu.dk/service.php?TargetP-
2.0
)
b. (0.3) DeepMito (
http://busca.biocomp.unibo.it/deepmito/
) c. (0.2) CELLO (
http://cello.life.nctu.edu.tw/
) - FASTA format only
d. (0.3) Predotar (
https://urgi.versailles.inra.fr/predotar/
)
TargetP
Protein type
Other
Likelihood
0.923
DeepMito
Predicted mitochondrial?
No
GO-term
Mitochondrial intermembrane space
Score
0.17
Localization
Periplasmic
CELLO
Reliability
1.348
Predotar
Mitochondrial
0,19
ER
0,00
Elsewhere
0,55
5. There is a file of ITPR3 cDNAs called itpr3.fst. Open MAFFT
and run the multiple alignment followed by the following alignment programs: NJ (both methods), UPGMA.
a. (0.2) What are ITPR3 proteins?
ITPR3 proteins are encoded by the ITPR3 gene. The protein encoded by this gene is a second messenger
that mediates the release of intracellular calcium.
b. (0.2) Comment on how reproducible the tree is using the different methods.
The trees are very similar. The length of the branches differ slightly.
c. (0.3) List all sister taxa for each tree
NJ (conserved)
5&6, 1&2
NJ(gap-free)
1&2, 5&6
UPGMA
1&2, 5&6
d. (0.1) Which tree topology do you think makes the most sense based on the organisms?
UPGMA
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CCT CCA GGT CGA CrC TAG AGG ATC CC GGG TAC CGA CCT CGA ATT CT MT CAT G07 CAT AGC TGT 7C CtG 3
ITA OTA CCA GTA TCI ACA ANG GC Y
3 C ATT TO Crs cOG
Lacz Val Val Al Leu
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