What is protein homology?
Protein homology is the study of relatedness and evolution of certain species through the examination of the commonalities of their proteins. When identical amino acid sequences have been found in two species it is often believed that the two share a common ancestor. Proteins in species that were once identical my diverge through gene duplications that lead to specific amino acid sequences being coded for inaccurately. These similarities and divergences allow us to make certain hypotheses about the evolutionary events that lead to contemporary proteins, and ultimately the connectedness of these organisms [1]. The protein homology field is critical because it has provided many advances in understanding how diseases function due to many studies in model organisms [2].
What are the homologs of the human AMPK-gamma-2 protein?
Putative homologs for the human AMPK-gamma-2 were found using the program BLAST. BLAST is a program that interprets sequences of genomic data and compares it to other species with sequenced genomes. It displays the results of other known species with significant protein sequence alignments and also allows you to pair up your sequence with any other species you're interested in [3]. The file below contains the protein sequences (in FASTA format) of the human AMPK-gamma-2 protein compared to the homologous protein sequences of thirteen other organisms (six of them being common research model organisms).
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List of Homologous Proteins
Homo sapiens (Human) - AMPK-gamma-2
Accession Number: NP_057287.2 GI: 33186925 FASTA Pan troglodytes (Chimpanzee) - 5'-AMP-activated protein kinase subunit gamma-2 isoform 3 Accession Number: XP_003318974.1 GI: 332870108 E Value: 0.0 Max. Identity: 99% FASTA Rattus norvegicus (Rat) - protein kinase, AMP activated, gamma 2 non-catalytic subunit, isoform CRA_a Accession Number: EDL86378.1 GI: 149031388 E Value: 0.0 Max. Identity: 99% FASTA Mus musculus (Mouse) - 5'-AMP-activated protein kinase subunit gamma-2 isoform 2 Accession Number: NP_001164026.1 GI: 282847327 E Value: 0.0 Max. Identity: 98% FASTA Bos taurus (Cattle) - 5'-AMP-activated protein kinase subunit gamma-2 Accession Number: XP_002687025.1 GI: 297474292 E Value: 0.0 Max. Identity: 97% FASTA Gallus gallus (Chicken) - 5'-AMP-activated protein kinase subunit gamma-2 Accession Number: NP_001026136.1 GI: 71896623 E Value: 0.0 Max. Identity: 96% FASTA Canis lupus familiaris (Dog) - 5'-AMP-activated protein kinase subunit gamma-2 Accession Number: XP_532769.3 GI: 345781415 E Value: 0.0 Max. Identity: 93% FASTA Xenopus tropicalis (Clawed Frog) - AMP-activated, gamma 1 non-catalytic subunit Accession Number: NP_001121411.1 GI: 189230174 E Value: 0.0 Max. Identity: 92% FASTA Felis catus (Cat) - 5'-AMP-activated protein kinase subunit gamma-2 isoform 1 Accession Number: XP_003983282.1 GI: 410953242 E Value: 0.0 Max. Identity: 91% FASTA Danio rerio (Zebrafish) - Uncharacterized Accession Number: XP_696730.3 GI: 189515661 E Value: 0.0 Max. Identity: 88% FASTA Caenorhabditis elegans - AAKG-1 Accession Number: NP_499637.2 GI: 71992475 E Value: 2e-114 Max. Identity: 55% FASTA |
What are the alignments of AMPK-gamma-2 protein?
Protein sequence alignments were performed on all 11 organisms using Clustal Omega and T-Coffee. These programs align significantly similar protein sequences to help identify conserved regions and help determine evolutionary relationships between organisms.
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Analysis
The color coding on both the Clustal Omega and T-Coffee alignments allows us to visualize the conserved protein sequences between the organisms. The BLASTed E values of the homologs emphasize what the protein alignments show--that this protein seems to be highly conserved among all 11 organisms. These small E values suggest a more significant score and alignment because they represent the number of different alignments with scores equivalent to or better than what is expected to occur by chance [3]. Because of the critical role that this protein plays in sensing and responding to energy demands within the cell, and regulating chemical pathways involved in the cell's main energy source (ATP), it makes sense for this protein to be highly conserved among all organisms [4].
References
[1] Doolittle, R. F. (1981). Similar Amino Acid Sequences: Chance or Common Ancestry? Science, 214(4517):149-59. DOI: 10.1126/science.7280687
[2] Manning, G., Whyte, D. B., Martinez, R., Hunter, T., Sudarsanam, S. (2002). The Protein Kinase Complement of the Human Genome. Science, 298:1912-34. DOI: 10.1126/science.1075762
[3] Altschul S.F., Gish W., Miller W., Myers E.W. and Lipman D.J. (1990) Basic local alignment search tool. Journal of Molecular Biology. 215: 403-410.
[4] Burwinkel, B., Scott, J.W., Buhrer, C., et al. (2005). Fatal congenital heart glycogenosis caused by a recurrent activating R531Q mutation in the gamma 2-subunit of AMP-activated protein kinase (PRKAG2), not by phosphorylase kinase deficiency. The American Journal of Human Genetics, 76(6): 1034-49. doi: 10.1086/430840
[2] Manning, G., Whyte, D. B., Martinez, R., Hunter, T., Sudarsanam, S. (2002). The Protein Kinase Complement of the Human Genome. Science, 298:1912-34. DOI: 10.1126/science.1075762
[3] Altschul S.F., Gish W., Miller W., Myers E.W. and Lipman D.J. (1990) Basic local alignment search tool. Journal of Molecular Biology. 215: 403-410.
[4] Burwinkel, B., Scott, J.W., Buhrer, C., et al. (2005). Fatal congenital heart glycogenosis caused by a recurrent activating R531Q mutation in the gamma 2-subunit of AMP-activated protein kinase (PRKAG2), not by phosphorylase kinase deficiency. The American Journal of Human Genetics, 76(6): 1034-49. doi: 10.1086/430840
Margaret Beatka ([email protected])
Page Last Updated: 5/10/13
This web page was produced as an assignment for Genetics 677, as an undergraduate course at UW-Madison.
Page Last Updated: 5/10/13
This web page was produced as an assignment for Genetics 677, as an undergraduate course at UW-Madison.