This web page was produced as an assignment for Genetics 677, an undergraduate course at UW-Madison.
Protein homologs
To identify the species with homologous proteins I used Homologene and BLAST databases.
Human [Homo sapiens]
Protein: fibroblast growth factor receptor 2 isoform 1 precursor Accession number: NP_000132.3 Dog [Canis lupus] Protein: fibroblast growth factor receptor 2 precursor Accession number: NP_001003336.1 Fly [Drosophilia melanogaster] Protein: breathless, isoform A Accession number: NP_729956.1 |
Mouse [Mus musculus]
Protein: fibroblast growth factor receptor 2 isoform IIIc Accession number: NP_034337.2 Zebrafish [Danio rerio] Protein: fibroblast growth factor receptor 2 isoform 3 precursorAccession number: NP_840088.2 |
Chicken [Gallus gallus]
Protein: fibroblast growth factor receptor 2 precursor Accession number: NP_990650.1 Bovine [Bos taurus] Protein: fibroblast growth factor receptor 2 Accession number: NP_001192239.1 |
Protein homolog alignments
T-Coffee (1,2) and ClustalW (3,4) were used to align the protein sequences and assess the homology of the protein across the species listed above.
Analysis
Both alignment programs were used with the FASTA format of the protein in each species. The T-Coffee alignment is most explicative because it uses a color spectrum to indicate how similar the separate protein sequences are. In the T-Coffee alignment, the overall homology score given to the homologous fgfr2 proteins is 92 of a possible 100. The least homologous protein was that of the fly, Drosophilia melanogaster which was given a score of 88. The Clusalw alignment is also listed, and the scores associated with the Clustalw alignment are in a separate document. These scores also indicate a high level of homology, as in the T-Coffee alignment.
References
1. Di Tommaso P, Moretti S, Xenarios I, Orobitg M, Montanyola A, Chang JM, Taly JF, Notredame C. T-Coffee: a web server for the multiple sequence alignment of protein and RNA sequences using structural information and homology extension. Nucleic Acids Res. 2011 Jul;39(Web Server issue):W13-7. Epub 2011 May 9.
PMID: 21558174
2.Notredame C, Higgins DG, Heringa J. T-Coffee: A novel method for fast and accurate multiple sequence alignment. J Mol Biol. 2000 Sep 8;302(1):205-17.
PMID: 10964570
3. Larkin MA, Blackshields G, Brown NP, Chenna R, McGettigan PA, McWilliam H, Valentin F, Wallace IM, Wilm A, Lopez R, Thompson JD, Gibson TJ, Higgins DG. (2007). Clustal W and Clustal X version 2.0. Bioinformatics, 23, 2947-2948
PMID:17846036
4. Thompson JD, Higgins DG, Gibson TJ. (1994). CLUSTAL W: improving the sensitivity of progressive multiple sequence alignment through sequence weighting, position-specific gap penalties and weight matrix choice. Nucleic Acids Res., 22, 4673-4680
PMID:7984417
PMID: 21558174
2.Notredame C, Higgins DG, Heringa J. T-Coffee: A novel method for fast and accurate multiple sequence alignment. J Mol Biol. 2000 Sep 8;302(1):205-17.
PMID: 10964570
3. Larkin MA, Blackshields G, Brown NP, Chenna R, McGettigan PA, McWilliam H, Valentin F, Wallace IM, Wilm A, Lopez R, Thompson JD, Gibson TJ, Higgins DG. (2007). Clustal W and Clustal X version 2.0. Bioinformatics, 23, 2947-2948
PMID:17846036
4. Thompson JD, Higgins DG, Gibson TJ. (1994). CLUSTAL W: improving the sensitivity of progressive multiple sequence alignment through sequence weighting, position-specific gap penalties and weight matrix choice. Nucleic Acids Res., 22, 4673-4680
PMID:7984417