Katie's Assignment
I am interested in exploring the genetic make up of enzymes that have been previously identified as being "salt dependent" for activity- such as citrate synthase, malic enzyme and aspartae transcarbamylase (which are all found in our species' genome).
What is citrate synthase and what is its role in our species?
What is malic enzyme (malate dehydrogenase) and what is its role in our species?
Why/How did I pick these three enzymes?
JGI Genes:
Citrate Synthase Gene from JGI:
Allosteric NADP-dependent Malic Enzyme
Aspartate carbamoyltransferase
Aspartate carbamoyltransferase 2
RAST Genes:
Aspartate carbamoyltransferase
Aspartate carbamoyltransferase regulatory chain
Main Tasks
1). Verify annotation of all genes from each annotation service: start and stop codon, SD sequence
JGI Genes:
Citrate Synthase -50 downstream bases: (red= stop and start codons, green= downstream bases)
2). Look for other genes in our species' genome that are similar and may have been missed during annotation
3). Note the pathways and systems that these genes play a role in
4). Look at the sequences from the halophile studied in the article as compared to these gene sequences
5). Find these genes in other halophiles in adopt a genome project and in the other 8 genomes of halophiles that have been annotated
6). Blast results of our species' genes: pick halophiles, bacteria, and eukarya to compare nucleotide sequence and protein sequence to (separate salt-loving and non-salt loving)
7). Look for differences in predicted protein structure and potential amino acid bias. (ClustalW)
8). Look for similarities between the genes for these 3 enzymes that are salt dependent.
