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?

What is aspartate transcarbamylase and what is its role in our species genome?

Why/How did I pick these three enzymes?

Citrate Synthase Gene from JGI:

>644032817 citrate synthase (EC 2.3.3.1) (IMGterm) [Halomicrobium mukohataei DSM 12286, unfinished sequence: NZ_ABTY01000001] (+)strand

ATGTCCGACGACCTCAAGCAAGGTCTGGAGGGTGTCCTCGTTACCGAGTC GGAGCTCAGCAAGATCGACGGTGACGCGGGCAAACTCGTCTATCGTGGCT ACACGATCGAGGACCTGGCGACCGGCGCAAGCTTCGAGGAGGTCCTGTAT CTCCTCTGGCACGGTCACCTCCCGAACGCAGCGGAGCTCGACGAGTTCAC CGACGCGATGGTCGAGGAGCGACACGTCGACGACGACGTCATGCAGACCG TCGAGCAGCTCGCCGACGCCGACGAGAATCCGATGGCCGCGCTCCGAACG GCGGTCTCGATGCTGTCCTCGCACGATCCCGACGCCGAAACCGACCCGAC CGACCTCGACGCCAACCTCCGGAAAGGTCGCCGGATCACCGCCAAGATCC CGACCGTGCTGGCTGCCTTCGCCCGGTTCCGTGACGGACAGGACGCCGTC GAACCGCGGGAAGACCTCTCGCACGCCGCGAACTTCCTCTACATGCTCAA CGGCGAGGCACCGGACGAGGTGCTCGCCGAGACGTTCGACATGGCGCTCG TGCTCCACGCCGACCACGGCATCAACGCCTCGACGTTCTCGGCCATGGTC ACGGCCTCGACGCTGTCGGATCTCCACAGCGCGATCACCTCCGCGATCGG CACCCTGAAGGGATCGCTCCACGGCGGCGCGAACCAGGACGTCATGGAGA TGCTCAAGGAGGTCGACGACGCCCAGCAGGACCCGATCGACTGGGTGAAG ACGGCACTCGACGAGGGACGGCGCGTCTCCGGCTTCGGCCACCGCGTCTA CAACGTCAAGGACCCCCGTGCGAAGATCCTCAGCCAGCGCTCGAAGGAAC TGGGGGAGGCCGCCGGCTCGCTCAAGTGGTACGAGATGTCCACCGCCATC GAGGACTACCTCAAAGCGGAGAAGGGGCTGGCCCCGAACGTCGACTTCTA CTCGGCCTCGACGTACTACCAGATGGGGATCCCCATCGACATCTACACTC CCATCTTCGCGATGTCCCGCGTCGGCGGCTGGACGGCCCACGTCCTCGAA CAGTACGAGAACAACCGTCTGATCCGGCCCCGCGCTCGCTACGTCGGCCC GACGGATCAGACGTTCGTCCCCCTCGACGAGCGATAG

Main Tasks

1). Verify annotation of all genes from each annotation service: start and stop codon, SD sequence

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). Find these genes in other halophiles in adopt a genome project and in the other 8 genomes of halophiles that have been annotated

5). Blast results of our species' genes: pick halophiles, bacteria, and eukarya to compare nucleotide sequence and protein sequence to

6). Look for differences in predicted protein structure and potential amino acid bias

7). Look for similarities between the genes for these 3 enzymes that are salt dependent.