Bioinformatics Assignment: Protein Structure and Function
Protein: FADD
MMDB Name: 2gf5
| Secondary Structure | Amino Acid Sequence | |
|---|---|---|
| 1 | Helix 1 | 3-14 |
| 2 | Helix 2 | 17-26 |
| 3 | Helix 3 | 44-52 |
| 4 | Helix 4 | 61-70 |
| 5 | Helix 5 | 74-84 |
| 6 | Helix 6 | 95-105 |
| 7 | Helix 7 | 112-119 |
| 8 | Helix 8 | 123-133 |
| 9 | Helix 9 | 138-152 |
| 10 | Helix 10 | 159-168 |
| 11 | Helix 11 | 172-189 |
DOMAINS OF FADD
FADD has two domains. The domains do not have any distinguishable functions. Each domain contains alpha helices.
The domains may be found in other proteins.
Domain 1- Related Protein Structures
Domain 2- Related Protein Structures
Conserved Domains in other proteins for FADD
VAST:
Screenshot of FADD and Structurally Related Neighbors
Amino Acid Sequences of Structurally Related Proteins for FADD
Secondary Structure for FADD and its Structurally Related Proteins
Is your protein secreted? No
Is it a transmembrane protein? No
Is the secondary structure predicted correctly? No. FADD has many alpha helices and the program did not detect them.
Did HmmrPfam find the other known domains you identified using the databases? This Failed.
How does a hydrophobicity plot predict protein structure? It helps to determine the protein structure because hydrophobic amino acids tend to aggregate around another. Although they may be dispersed througout the sequence, they still attempt to unite, which may suggest the formation of an alpha helix or a beta sheet.
| Program | Parameters |
|---|---|
| CoilScan | Default |
| HelicalWheel | Default |
| HmmerPfam- failed | Default |
| HTHScan | Default |
| Isoelectric | Default |
| Moment | Default |
| PepPlot | Default |
| PeptideSort | Default |
| PeptideStructure | Default |
| SPScan | Default |
| TransMem | Default |
PDB and Entrez are both very good protein databases. The links to these databases for the FADD gene can be found on the FADD page.