Difference between revisions of "Uncharacterized Protein Family (UPF0153) (Katie Richeson)"
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== Blastx Search== | == Blastx Search== | ||
| + | The results of the blastx search gave many hypothetical proteins or just unknown protein functions. Although, the third hit from [http://www.ncbi.nlm.nih.gov/sites/entrez?cmd=Retrieve&db=protein&dopt=GenPept&RID=ABA7AD9G01S&log%24=prottop&blast_rank=3&list_uids=227880107 Halogeometricum borinquense] was a predicted predicted Fe-S [http://en.wikipedia.org/wiki/Oxidoreductase oxidoreductas]e, which is an enzyme that catalyses the transfer of Iron and Sulfide ions from one molecule to another. | ||
| + | |||
| + | == GC Content == | ||
| + | The GC content for this gene is [http://img.jgi.doe.gov/cgi-bin/geba/main.cgi?section=GeneDetail&page=geneDetail&gene_oid=644030411 68%] and the GC content for our species' genome is 65%. Therefore it is unlikely that this gene is an alien gene, but does not rule out the possibility of orthologs or paralogs. | ||
| + | |||
| + | == Genome Portal Results with Other Halophiles == | ||
| + | I found similar nucleotide sequences in other halophiles using the blast aspect in [http://genome.jgi-psf.org/ genome portal] with different halophiles. But these halophiles have not been annotated as of yet so the similar nucleotide sequences did not provide any additional data. | ||
| + | |||
| + | == Codon Bias == | ||
| + | I would like to see if the codon bias for this gene shows any sort of relation to our species or another species but I do not know how to check this. | ||
Latest revision as of 01:02, 8 September 2009
Contents
Uncharacterized Protein Family (644030411)
Blastn Search
No helpful results, all complete genomes. Shows that this nucleotide sequence is found in many halophiles such as Halorubrum lacusprofundi.
Blastx Search
The results of the blastx search gave many hypothetical proteins or just unknown protein functions. Although, the third hit from Halogeometricum borinquense was a predicted predicted Fe-S oxidoreductase, which is an enzyme that catalyses the transfer of Iron and Sulfide ions from one molecule to another.
GC Content
The GC content for this gene is 68% and the GC content for our species' genome is 65%. Therefore it is unlikely that this gene is an alien gene, but does not rule out the possibility of orthologs or paralogs.
Genome Portal Results with Other Halophiles
I found similar nucleotide sequences in other halophiles using the blast aspect in genome portal with different halophiles. But these halophiles have not been annotated as of yet so the similar nucleotide sequences did not provide any additional data.
Codon Bias
I would like to see if the codon bias for this gene shows any sort of relation to our species or another species but I do not know how to check this.
