Download Gene fusion analysis

Steps in analyzing fusions of domains to known enzymes
Triage into ‘essentially known’, ‘unknown and unpromising’, and ‘unknown and promising’ categories
1. Is the fusion real, i.e. does it occur in several independent genomes? (Run a Blast search at NCBI.)
Are those genomes high-quality? Those that are *not* high quality include many non-model fungal
genomes, and prokaryote genomes with >100 contigs.
2. Is the fused domain most probably a known enzyme? (Use Seq2Ref, PubMed, etc.) If so, discard.
3. Does the fusion protein have more than one unknown domain? (This usually triggers discard.)
4. Is the unknown fusion domain enzyme-like? (Transporter-like domains are of less interest; probable
regulatory or membrane-anchor domains trigger discard.)
5. Is the known enzyme in the fusion protein the only copy in the genome? (In SEED, Blast the fusion
sequence against the genome it comes from.)
6. If there is more than one copy, is the fused copy an ortholog of the canonical enzyme or a paralog?
(Examine clustering patterns with other enzymes of same pathway, examine phylogenetic trees.) (If the
fusion is to a paralog of the canonical enzyme, this could trigger discard.)
7. Does the unknown domain occur as a stand-alone protein? (Evident from Blast search and trees.)
8. If so, what do the genes encoding the stand-alone protein cluster with? (Evident from SEED compare
regions tool.)
9. How taxonomically diverse are the organisms where the fused or stand-alone unknown occurs? (The
more diverse the organisms, the more retention is favored), and do they include plants?
10. What reaction does the known enzyme in the fusion mediate and what is its catalytic chemistry?
(Essential context for imagining a function for the unknown domain.)
11. What type of reactions do CDD, pfam, structure prediction programs (Phyre, GenThreader), and the
literature, indicate that the unknown protein might do?
12. Can this type of reaction be rationally connected to the activity of the known fusion partner?
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