Talk Talk Wee (TTW) You're Dead already... But you brought me with you.. DAMN!!!

Why am I saying this? The exams are already over, but then TTW killed me... For the last time of my life (hopefully) I will demonstrate what I learn from LSM2104. I'm just glad that the exams are over and I can play with ease... Now the next thing is to plan my schedules... Hmmm...

I was wondering whether how special our genetic pool is, whether there is anything special with the genes. Come to think of it, why not I try to test my gene-line. Would I survive this paper? Would it kill me? Lets see...

I want to see whether the protein "IWILLDIEONBIOINFORMATICS" exist in me and whether there is a protein structure on it. After that, infer to the rest of the human species whether they will die with me in the paper. SO... I took the protein and use BLAST it with pdbaa, using settings BLOSUM62, blastp and unchecked the low complexity to prevent masking of low complexity portions.


The results are shown below:

The best hit has the ID gi|55670668|pdb|1WD4|A Chain A, Crystal Structure of Arabinofuranosidase Complexed with Arabinose Chain A, Crystal Structure of Arabinofuranosidase. Though the E-value and score isn't that all good, it's good identities and positives would state that there is probably a conservation of function in that region. So after that, I went to PDB to search for the structure of the protein, 1WD4. The results are stated below:

I click on the ligand interaction view link to spot for ligands that probably interact with the protein. Then I downloaded the PDB file to indicate the regions of the binding site of the ligand. The results are stated below:


Interesting huh? Hmmm... The region must be responsible for our death when in contact with the paper. To double confirm my hypothesis, I must go to KEGG pathway to search for all pathways that might involve humans. Thus, KEGG pathway here I come...

At KEGG pathway, I search for Arabinofuranosidase and I click on the proper result. I found out that the protein came from map00520 and it is from enzyme 3.2.1.55. The picture is stated below:

HEY!!! It doesn't contain human pathway!!! Yeah!!! That means that we won't die in the paper afterall!!! Hmmm... lets go a little further. The protein seems to be from a bacteria. The taxonomy linage, prosite pattern region and sequence can be seen below in the pictures:


Maybe we won't be dying in the hall afterall... Maybe I shouldn't be worrying too much since it's not in our genes... HAHAHA...





















But you know what? I couldn't do any of the questions in the paper.... -_-||| Damn... It managed to kill me... Maybe it's that bacteria!!!



Note: The method to do protein/homology analysis is not the correct protocol. What is stated is purely for entertainment. I wish to apologise to anyone who argues profusiously about my nonsense. =) Enjoy. Thank you for your audience.

References:
==> BLAST- http://www.ncbi.nlm.nih.gov/BLAST/Blast.cgi
==> Protein Database (PDB) - www.rcsb.org/pdb
==> KEGG pathway - www.genome.jp/KEGG
==> Ligand Explorer
==> Rasmol standalone

==> National Center for Biotechnology Information Taxonomy linage - http://www.ncbi.nlm.nih.gov/Taxonomy

DONE WITH EXAMS AND ENJOYING HIS FREEDOM
The Mixed Boy