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Answer:

1. Query the information about protein trpA ( Tryptophan synthase alpha chain in Salmonella typhimurium ) in DIP database. What is (are) the interaction partner(s) and what is the method used to discover the interaction(s)?. Answer:

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  1. 1. Query the information about protein trpA (Tryptophan synthase alpha chain in Salmonella typhimurium) in DIP database. What is (are) the interaction partner(s) and what is the method used to discover the interaction(s)? Answer: There is only one interaction. The partner is tryptophan synthase beta chain. The interaction is discovered by using x-ray crystallography

  2. 2. What is the protein complex in human containing protein AHR? What is the method used to discover this complex? What is the publication supporting this result?. Answer: AHR belongs to the complex: Ubiquitin E3 ligase in human. This complex was discovered by co-immunoprecipitation method. This result is supported by the paper "Dioxin receptor is a ligand-dependent E3 ubiquitin ligase" by Ohtake F.et.al. in Nature 2007

  3. 3. Use STRING database to see if panD occurs in the conserved gene neighborhood in the E. Coli genome. Find out the neighbours of panD in that genomic region Answer: PanB and PanC are close in the genomic region. Sequences are in a row next to each other suggesting that they form an operon

  4. 4. For PanD, go to the text mining. Expand all the E. Coli related abstracts in the view. Which of the article shows strongest support to the functional linking? Is there any article that is only a false positive link to other proteins?. Answer: For PanD, the 4th article: "Towards engineering increased pantothenate (vitamin B(5)) levels in plants." shows strongest support. It shows a well-establish pathway containing three proteins panD, panB and panC. The 5th article: "Pantothenate biosynthesis in higher plants." seems to be false positive support.

  5. 5. What is the homology of panB in Saccharomyces cerevisiae?. What is the bit score?. Answer: Best similarity hit of panB in species Saccharomyces cerevisiae: ECM31 (3-methyl-2-oxobutanoate hydroxymethyltransferase(EC 2.1.2.11) (Ketopantoate hydroxymethyltransferase) (Extracellular matrix protein 31) ). Score 160.0 bits.

  6. 6. Can you see fusion proteins of leuC ? In what species they occur Answer: There are fusion proteins including leuD in Dikarya (a subkingdom of Fungi) and acnA in Spermophilus tridecemlineatus and Protochlamydia

  7. 7. Which are strong co-expressed genes of leuC in E. Coli K12 Answer: They are leuA, leuB and leuD

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