Forum "Conclusion"

Thread subject: TO9D_5914020 Genomic DNA (: Algiers-Barcelona station 9 DCM)

[ Return to forums ]
TO9D_5914020 Genomic DNA (: Algiers-Barcelona station 9 DCM)
24 Jun 2016 16:50
Non evaluated contribution

In frame -1, negative sense: 3’ to 5’, from the first nucleotide position, an ORF was found from nucleotide 737 to nucleotide 3. No start codons were found in the selected ORF. The ORF is translated into 244 amino acids. It is an incomplete ORF due to the lack of start and stop codons.

Query sequence was further analysed using ExPASy Translate Tool to locate start codons and stop codons, to find a more complete ORF. However when these ORFs were analysed through BLAST, they had inferior BLAST results compared to the initial selected ORF from Fig. 1: lowest E-value with highest max score. 

Using ‘Compute pI/Mw’, derived protein from the sequence is theoretically: Molecular weight (Da): 35471.39 (average mass), 35449.61 (monoisotopic mass) Theoretical pI: 3.22. Protein may be isolated via gel electrophoresis with the following data.

SWISS-MODEL predictions have lesser than 20% matches.

When checked with PROPSEARCH. The qualities of the matches are calculated by DIST e.g.  0.0 to 1.3 has 99.9% reliability and 8.7 to 10.0 have 87% reliability. The closer matches of 80% reliability are the hypothetical proteins in yeast (VOA1_Yeast : Saccharomyces arboricola) and nematode (Caenorhabditis elegans) since the pI is closer to the theoretical pI of 3.22

Interpro analysis did not recognise the protein sequence translated from the ORF.

Using PSORTb, searching under Archaea and Gram-negative (assuming it is indeed from the flavobacteriia family) yielded no hits but a score of 7.5 and more predicted that the coded protein will be in the cytoplasm.

The query sequence aligned to organisms under the flavobacteriia family, but has more homology towards Lacinutrix sp. Due to the lack of alignment to any known conserved domains, the sequence does not code for any proteins that is in the database yet and may need to undergo further analysis or tests to understand its function or structure.