Saturday, April 11, 2009

~ steps get to our bacteria ~

we have been given a task to find our bacteria based on some information....
  • part of DNA sequence
  • part of protein sequence
  • gene position
  • and some other information
below are the steps to get approach to our lovely bacteria~~~ ♥
  1. Go to BLAST website (click on the BLAST link)
  2. Click the Nucleotide Blast which under the topic Basic Blast
  3. Paste the partial DNA sequence on "Enter Query Sequence"
  4. Choose Nucleotide collection (nr/nt) under "Choose Search Set -Database"
  5. Click on BLAST when you are finish all the step above.
  6. A list of bacteria or organisms will be listed out.
  7. The 1st organism in the list is our LOVELY ORGANISM - Mycoplasma pneumoniae 's adhesion protein

LOCUS       EF614306                 825 bp    DNA     linear   BCT 18-MAR-2008
DEFINITION Mycoplasma pneumoniae adhesin protein (P30) gene, complete cds.
VERSION EF614306.1 GI:148729625
SOURCE Mycoplasma pneumoniae
ORGANISM Mycoplasma pneumoniae
Bacteria; Tenericutes; Mollicutes; Mycoplasmataceae; Mycoplasma.
REFERENCE 1 (bases 1 to 825)
FEATURES Location/Qualifiers
source 1..825
/organism="Mycoplasma pneumoniae"
/mol_type="genomic DNA"
/isolation_source="clinical sample"
gene 1..825
CDS 1..825
/product="adhesin protein"
1 atgaagttac cacctcgaag aaagcttaaa ctgtttttat tagcctgaat gctagtgctg
61 ttcagcgctt taatagtgct tgcaacctta attttggtac agcacaacaa taccgaactg
121 acagaagtta agagtgaatt gagtcccctt aacgttgttt tacacgcaga agaggataca
181 gtacaaattc agggcaagcc gattactgag caagcatggt ttattcctac agttgctggt
241 tgctttggtt ttagtgccct agccatcatc ttgggccttg ctataggact gccaattgtg
301 aagcgcaagg aaaaacgctt atcggaggaa aaggaacgcc aagaacagtt agcggaacag
361 ctacaacgca tttctgccca acaagaagag caacaagcgt tagaacaaca agcagctgct
421 gaagcccatg ctgaagcgga agttgaacca gcaccacaac cagtaccagt accacctcaa
481 ccccaagtcc aaattaactt cggtccccgt actggtttcc cacctcaacc cggtatggcg
541 cctcgtccag gtatgccgcc acaccccggt atggctccaa gatctggttt cccacctcaa
601 cccggtatgg cgcctcgtcc aggtatgccg ccacaccccg gtatggctcc aagacctggt
661 ttcccacctc aacccggtat ggcgcctcgt ccaggtatgc cgccacaccc cggtatggct
721 ccaagacctg gtttcccacc tcaacccggt atggcgcctc gtcccggaat gcaaccacca
781 cgtcctggca tgccacccca acccggtttt ccaccaaaac gctaa

finally~~ we get the protein~~~ and our bacteria ~~~ ♥


This diagram shows proteins in Mycoplasma pneumoniae and how they link with each other.
Adhesin protein, ATP synthase and other proteins are found at the cell membrane.
3D structure of the protein also can be seen in this diagram.