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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.
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 liganddependent E3 ubiquitin ligase" by Ohtake F. et.al. in Nature 2007
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.
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.
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.
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.
Which are strong co-expressed genes of leuC in E. Coli K12
Answer:
They are leuA, leuB and leuD