Difference between revisions of "Katie's Assignment"
Karicheson (talk | contribs) |
Karicheson (talk | contribs) |
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JGI Genes: | JGI Genes: | ||
| − | [http://img.jgi.doe.gov/cgi-bin/geba/main.cgi?section=GeneDetail&page=geneDetail&gene_oid=644032817 Citrate Synthase JGI: 2916896..2918032 (+) (1137bp)]. . . [http://img.jgi.doe.gov/cgi-bin/geba/main.cgi?exportGenes=1&exportType=nucleic&gene_oid=644032817&up_stream=0&down_stream=0 nucleotide | + | [http://img.jgi.doe.gov/cgi-bin/geba/main.cgi?section=GeneDetail&page=geneDetail&gene_oid=644032817 Citrate Synthase JGI: 2916896..2918032 (+) (1137bp)]. . . [http://img.jgi.doe.gov/cgi-bin/geba/main.cgi?exportGenes=1&exportType=nucleic&gene_oid=644032817&up_stream=0&down_stream=0 nucleotide sequence] |
| − | [http://img.jgi.doe.gov/cgi-bin/geba/main.cgi?section=GeneDetail&page=geneDetail&gene_oid=644031893 Allosteric NADP-dependent Malic Enzyme 2055313..2057565 (+) (2253bp)] . . . [http://img.jgi.doe.gov/cgi-bin/geba/main.cgi?exportGenes=1&exportType=nucleic&gene_oid=644031893&up_stream=0&down_stream=0 nucleotide | + | [http://img.jgi.doe.gov/cgi-bin/geba/main.cgi?section=GeneDetail&page=geneDetail&gene_oid=644031893 Allosteric NADP-dependent Malic Enzyme 2055313..2057565 (+) (2253bp)] . . . [http://img.jgi.doe.gov/cgi-bin/geba/main.cgi?exportGenes=1&exportType=nucleic&gene_oid=644031893&up_stream=0&down_stream=0 nucleotide sequence] |
[http://img.jgi.doe.gov/cgi-bin/geba/main.cgi?section=GeneDetail&page=geneDetail&gene_oid=644031330 Aspartate carbamoyltransferase regulatory subunit: 1503175..1503639 (-) (465bp)]. . . [http://img.jgi.doe.gov/cgi-bin/geba/main.cgi?exportGenes=1&exportType=nucleic&gene_oid=644031330&up_stream=0&down_stream=0 sequence] | [http://img.jgi.doe.gov/cgi-bin/geba/main.cgi?section=GeneDetail&page=geneDetail&gene_oid=644031330 Aspartate carbamoyltransferase regulatory subunit: 1503175..1503639 (-) (465bp)]. . . [http://img.jgi.doe.gov/cgi-bin/geba/main.cgi?exportGenes=1&exportType=nucleic&gene_oid=644031330&up_stream=0&down_stream=0 sequence] | ||
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RAST Genes: | RAST Genes: | ||
| − | [http://rast.nmpdr.org/seedviewer.cgi?page=Annotation&feature=fig|485914.5.peg.3029 Citrate Synthase TCA Cycle]. . . [http://rast.nmpdr.org/seedviewer.cgi?page=ShowSeqs&feature=fig|485914.5.peg.3029&Sequence=DNA%20Sequence sequence] | + | [http://rast.nmpdr.org/seedviewer.cgi?page=Annotation&feature=fig|485914.5.peg.3029 Citrate Synthase TCA Cycle]. . . [http://rast.nmpdr.org/seedviewer.cgi?page=ShowSeqs&feature=fig|485914.5.peg.3029&Sequence=DNA%20Sequence sequence] . . . [http://rast.nmpdr.org/seedviewer.cgi protein sequence] |
| − | [http://rast.nmpdr.org/seedviewer.cgi?page=ShowSeqs&feature=fig|485914.5.peg.3029&Sequence=DNA%20Sequence Citrate Synthase Glyoxylate Synthesis] | + | [http://rast.nmpdr.org/seedviewer.cgi?page=ShowSeqs&feature=fig|485914.5.peg.3029&Sequence=DNA%20Sequence Citrate Synthase Glyoxylate Synthesis] . . . [http://rast.nmpdr.org/seedviewer.cgi protein sequence] |
| − | [http://rast.nmpdr.org/seedviewer.cgi?page=ShowSeqs&feature=fig|485914.5.peg.2113&Sequence=DNA%20Sequence NADP-dependent malic enzyme] | + | [http://rast.nmpdr.org/seedviewer.cgi?page=ShowSeqs&feature=fig|485914.5.peg.2113&Sequence=DNA%20Sequence NADP-dependent malic enzyme]. . . [http://rast.nmpdr.org/seedviewer.cgi protein sequence] |
[http://rast.nmpdr.org/seedviewer.cgi?page=ShowSeqs&feature=fig|485914.5.peg.1562&Sequence=DNA%20Sequence Aspartate carbamoyltransferase] | [http://rast.nmpdr.org/seedviewer.cgi?page=ShowSeqs&feature=fig|485914.5.peg.1562&Sequence=DNA%20Sequence Aspartate carbamoyltransferase] | ||
Revision as of 20:46, 26 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 JGI: 2916896..2918032 (+) (1137bp). . . nucleotide sequence
Allosteric NADP-dependent Malic Enzyme 2055313..2057565 (+) (2253bp) . . . nucleotide sequence
Aspartate carbamoyltransferase regulatory subunit: 1503175..1503639 (-) (465bp). . . sequence
carbamoyltransferase: 1503636..1504550 (-) (915bp) . . . sequence
RAST Genes:
Citrate Synthase TCA Cycle. . . sequence . . . protein sequence
Citrate Synthase Glyoxylate Synthesis . . . protein sequence
NADP-dependent malic enzyme. . . protein sequence
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
Citrate Synthase blasted against our genome using Genome Portal: Two hits that are small but maybe a conserved region between the three enzymes that makes them salt dependent. Note that the subject alignments do not fall within any of the other two genes we are studying and thus this correlated sequence within our species' genome is not from one of the other salt dependent enzyme genes.
Malic Enzyme blasted against our species' genome using Genome Portal: Three hits shown below:
Aspartate carbamoyltransferase blasted against our species' genome using Genome Portal, results are below: (no hits besides the original gene)
Aspartate carbamoyltransferase regulatory unit blasted against out species' genome using Genome Portal, results are below: (no other hits besides the original gene)
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.
