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Forum "Conclusion"

Thread subject: Annotathon report 18601881

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Annotathon report 18601881
24 Jun 2016 17:34
Non evaluated contribution

The ORF Finder finds all open reading frames of a selectable minimum size in a user's sequence or in a sequence already in the database. It identifies all open reading frames using the standard or alternative genetic codes. Frame +1 sequence indicates a 5' to 3' shows 145 amino acids(aa) and with a start codon ATG(highlighted in blue) and a stop codon TGA(highlighted in pink) therefore is a complete strand.

From the Blast results page we can perform a multiple sequence alignment to verify that the ORF integrates convincingly in its presumed homolog family. The E-value indicates the number of hits one can expect to see by chance when searching a database of a particular size.

From the phylogenetic tree view(figure 9), we can see that the unnamed protein is closely related to the ABC-type branched-chain amino acid transport systems, ATPase component [Candidatus Actinomarina minuta].

Using compute pl/Mw for 5’3’ Frame 1, the molecular weight of the sequence is 16482.13 (average mass), 16471.62 (monoisotopic mass) and with theoretical pl of 7.89. 

In order to ensure that the finding for frame +1 sequence is correct, we use frame +3 sequence to compare our results. From the Blast results obtained for frame +1 (figure 6) and frame +3 (figure 13), the common protein is from ABC-type branched-chain amino acid transport systems, ATPase component [Candidatus Actinomarina minuta] due to the low E-value and high identity score.

Using the ORF finder, we are able to 4 types of frame sequences (frame +1,-1,+3,-2) and a positive frame indicates that it is a 5’ to 3’ sequence while a negative frame indicates a 3’ to 5’ sequence. We run the sequence with ExPASy translate and uses 5’3’ frame 1 to find out the molecular weight of sequence using compute pI/Mw. Furthermore, SWISS-MODEL allows us to visualize the structure of the sequence and the identity, in this case it is an ABC transporter.