Difference between revisions of "Katie's Assignment"
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'''1). Verify annotation of all genes from each annotation service: start and stop codon, SD sequence, are the genes different between the annotation services? | '''1). Verify annotation of all genes from each annotation service: start and stop codon, SD sequence, are the genes different between the annotation services? | ||
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JGI Genes: | JGI Genes: | ||
Revision as of 16:45, 24 September 2009
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 regulatory subunit
Aspartate carbamoyltransferase
RAST Genes:
Citrate Synthase Glyoxylate Synthesis
Aspartate carbamoyltransferase
Aspartate carbamoyltransferase regulatory chain
Main Tasks
1). Verify annotation of all genes from each annotation service: start and stop codon, SD sequence, are the genes different between the annotation services?
JGI Genes:
Citrate Synthase -50 downstream bases: (red= stop and start codons, green= downstream bases)
The two citrate synthase genes annotated from RAST are the same gene. . . below are the nucleotide blast alignment results:
The citrate synthase gene from JGI matches the citrate synthase genes from RAST, nucleotide blast alignment dot plot is below:
The aspartate carbamoyltransferase regulatory gene sequences are a 100% match between the two annotation services.
The aspartate carbamoyltransferase gene sequences are the same between both annotation services as well.
The malic enzyme genes are 100% the same between the two annotation services as well.
I also checked to see if the aspartate carbamoyltransferase regulatory subunit was part of the aspartate carbamoyltransferase gene but it was not as confirmed by blastn with alignment and the nucleotide base regions where the gene occurs.
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.
