Graded HW 2 (1) (1)

Name: Danyael Murphy Weeks 2-3: Graded Homework 2 1. (1 point) The following paper appeared in PubMed in 2021: “Experimental and computational investigation of enzyme functional annotations uncovers misannotation in the EC 1.1.3.15 enzyme class.” Find all proteins in the NCBI protein database with that enzyme commission number, limited to the organism, Diplocarpon rosae . a. (0.4) Clearly write the search strategy. 1.1.3.15 [ECNO] AND Diplocarpon rosae b. (0.3) How many records? 2 c. (0.3) List all protein lengths. 382, 160 2. (1) Find the nucleotide record with the accession number NM_005368.3. a. (0.2) How is this sequence described in the definition field? Homo sapiens myoglobin (MB), transcript variant 1, mRNA b. (0.2) How many exons are annotated in the Features table. 3 c. (0.2) What is the numerical location of the poly A signal? 1070 d. (0.2) Look at the revision history. On what date did the sequence most recently change? Nov 22, 2018 e. (0.2) Compare the before and after for the sequence change. How many nucleotides were removed? 8

3. (1) Enter “plant disease” into MeSH. a. (0.2) What is the preferred MeSH term? Diseases of Plants b. (0.2) Select the genetics subheader. Add to the search builder and then search PubMed. How many records? 1066 c. (0.2) Add an author named Zhao (as a first author) to the previous search. How many results? 89 d. (0.2) In the results, find a 2021 paper from Plant Cell Environ . GmST1 confers resistance to what strains of soybean mosaic virus G2 and G3 e. (0.2) Scroll down to related information and select protein. On what chromosome is the gene coding for this protein? 3 4. (1) Find the human NOD2 gene in the Gene database at NCBI. a. (0.2) According to the summary, mutations in this gene are associated with what diseases? Crohn disease and Blau syndrome b. (0.2) Examine the transcript table. How many of the transcripts do not code for protein? 5 c. (0.2) How many confirmed protein isoforms are listed. Do not count the predicted ones that start with “X.” 3 d. (0.2) Click the OMIM link on the right menu. Then open the Yao Syndrome record. From the Molecular Genetics section, how many patients carried the R702W variant in NOD2? 8 e. (0.2) According to Yao et al., what is the estimated population prevalence in the American adult population? 1 to 10 per 100,000 5. (1) Find Cutibacterium in the NCBI Taxonomy database. a. (0.2) List the domain (superkingdom) name. Bacteria b. (0.2) List the phylum name. Actinomycetota c. (0.3) Click on Cutibacterium acnes C1 . The prior name of this organism is listed as “heterotypic synonym.” What is that former name? Propionibacterium acnes C1 d. (0.3) How many direct links to the protein 4,691