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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