This web page was produced as an assignment for an undergraduate course at Davidson College. My Favorite Yeast Gene Annotated vs. Unannotated By Jessica Lahre
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Annotated Gene: SSH1/YBR283C The annotated gene SSH1 or YBR283C is located chromosome II of Saccharomyces cerevisiae between consisting of bases 770411-768939. SSH1 has the ORF name YBR2020 and is present in 704 molecules/cell. SSH1 gene encodes for the alpha-subunit of the SSH1 translocon complex in the endoplasmic reticulum called SSH1p or Sec61 protein homolog (SGD YBR283C: Summary 2006; UniPort P38353 2006; Finke et al. 1996). Its function involves protein transport, co-translational targeting, and probable maintenance of telomeres (SGD). The SSH1p has 490 amino acids with a molecular weight of 53,311 Da and an isoelectric point of 8.18 (UniPort P38353). Figure 1. Saccharomyces cerevisiae Chromosome II. This ORF map of Chromosome IIof Saccharomyces cerevisiae taken from SGD shows SSH1 gene (in blue) and YBR285W (in red). Image from http://db.yeastgenome.org/cgi-bin/ORFMAP/ORFmap?dbid=S000000487. SSH1 Amino Acid Sequence: MSGFRLIDIV KPILPILPEV ELPFEKLP DKIVYTIFAG LIYLFAQFPL VGLPKATTPN VNDPIYFLRG VFGCEPRTLL EFGLFPNISS GLILQLLAGL KVIKVNFKIQ SDRELFQSLT KVFAIVQYVI LTNIFIFAGY FGDDLSVVQI GLINFQLVGA GIFTTLLAEV IDKGFGFSSG AMIINTVVIA TNLVADTFGV SQIKVGEDDQ TEAQGALINL IQGLRSKHKT FIGGIISAFN RDYLPNLTTT IIVLAIAIIV CYLQSVRVEL PIRSTRARGT NNVYPIKLLY TGCLSVLFSY TILFYIHIFA FVLIQLVAKN EPTHIICKIM GHYENANNLL AVPTFPLSLL APPTSFFKGV TQQPLTFITY SAFILVTGIW FADKWQAISG SSARDVALEF KDQGITLMGR REQNVAKELN KVIPIAAVTG ASVLSLITVI GESLGLKGKA AGIVVGIAGG FSLLEVITIE YQQSGGQSAL NQVLGVPGAM (Sequence from http://db.yeastgenome.org/cgi-bin/protein/proteinPage.pl?dbid=S000000487) |
Cellular Component Figure 2. SSH1 Kyte-Doolittle Hydropathy Plot. The Kyte-Doolittle Hydropathy Plot from SGD shows here that there are 9 potential domains were transmembranes are located on the SSH1 protein. You can also see the similarities bettween SSH1 and the Sec61 proteins. Image from http://db.yeastgenome.org/cgi-bin/protein/domainPage.pl?dbid=S000000487. |
Biological Process |
Molecular Function |
Unannotated Gene: YBR285W The unannotated gene is YBR285W, located in the same region of chromosome II as SSH1 of Saccharomyces cerevisiae as shown in figure 1. The protein that YBR285 encodes for has 144 amino acids, a molecular weight of 16,833 Da, and an isoelectric point of 7.95 (UniPort P38354). The cellular component, biological process, and molecular function of YBR285Wp is unknown. YBR285W Amino Acid Sequence: mtifsrfsyf dslfsfkkqe pspieiiycn enngfiniks lesptddsme adishremat iltrnrnnlg kvaidkkgvn nhcidlnelk kglvanehkl dndnstrhqn tyspedsvef drfddkqsri lkcstrrsyl rykk (Sequence from http://db.yeastgenome.org/cgi-bin/protein/proteinPage.pl?dbid=S000000489. |
Cellular Component Figure 3. YBR285 Kyte-Doolittle Hydropathy Plot. This Kyte-Doolittle Hydropathy Plot of YBR285W, which shows domains of YBR285p that are most likely transmembrane domains. Peaks above 1.8 on this 19 window size would mean a transmembrane. (Kyte-Doolittle 2006) |
Biological Process and Molecular Function The BLASTp search brought up YBR287W found in Saccharomyces cerevisiae before YBR285W. Figure4. BLASTp results for YBR285W amino acid sequence.The results from the BLASTp YBR285W amino acid sequence displayed YBR287W before YBR285W. |
References Finke, K. et al. (1996). A second trimeric complex containing homologs of Sec61p complex function in protein transport across the ER membrane of S. cerevisiae. The EMBO Journal. 3 (7): 1482-1492 Kye-Doolittle Hydopathy Plot. <http://gcat.davidson.edu/DGPB/kd/kyte-doolittle.htm>. Accessed 2006 Oct 5. [NCBI] National Center for Biological Technology. 2006 Sept. <http://www.ncbi.nlm.nih.gov/>. Accessed 2006 Oct 2. SGD. 2006 Oct. SSH1/YBR283C: SGD ORF Map.<http://db.yeastgenome.org/cgi-bin/ORFMAP/ORFmap?dbid=S000000487>.Accessed 2006 Oct. 4. SGD. 2006 Oct. SSH1/YBR283C: Protein.<http://db.yeastgenome.org/cgi-bin/protein/domainPage.pl?dbid=S000000487>.Accessed 2006 Oct. 2. SGD. 2006 Oct. SSH1/YBR283C: Summary.<http://db.yeastgenome.org/cgi-bin/locus.pl?locus=SSH1>.Accessed 2006 Oct. 2. SGD. 2006 Oct. YBR285W: Protein.<http://db.yeastgenome.org/cgi-bin/protein/proteinPage.pl?dbid=S000000489>.Accessed 2006 Oct. 2. SGD. 2006 Oct. YBR285W: Summary.<http://db.yeastgenome.org/cgi-bin/locus.pl?dbid=S000000489>.Accessed 2006 Oct. 2. SSDB. 2006. SSDB KEGG Saccharomyces cerevisiae YJL029C.<http://www.genome.jp/dbget-bin/www_bget?sce:YJL029C>. Accessed 2006 Oct. 5. SSDB. 2006. SSDB Paralog Search. <http://www.genome.jp/ssdb-bin/ssdb_paralog?org_gene=sce:YBR285W>. Accessed 2006 Oct. 5. [UniPort]Universal Protein Resource.2006. P38354. <http://www.pir.uniprot.org/cgi-bin/upEntry?id=P38354 >. Accessed 2006 Oct. 5. [UniPort]Universal Protein Resource.2006. P38353. <http://www.pir.uniprot.org/cgi-bin/upEntry?id=P38353>. Accessed 2006 Oct. 5. |
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