Huynh 1
Bioinformation Lab Report
Name: Tony Huynh
Course: BIO3810
Date: April 12th 2024
Instructor: Toba Omotosho
Huynh 2
Result
In this experiment, 9 different organisms were conducted including: Streptococcus suis,
Streptococcus pneumoniae, Streptococcus mutans, Staphylococcus haemolyticus, Staphylococcus
aureus, Thermoplasma acidophilum, Clostridium botulinum, Clostridium tetani, and Clostridium
butyricum. After using NCBI to pick for the DNA topoisomerases of each organisms, Clustal
Omega were used to determine the Phylogenetic Tree. After, Phylogenetic Tree were used to
determine the two closest related organisms which were Clostridium tetani and Clostridium
butyricum. Both sequences of the two organisms were then used to create alignment to determine
the factors of its.
There were several identical amino acids between C. Tetani and C. Butyricum ( Table 1). We
used the colon “:” to determine the strongly similar molecular properties, which we were able to
find at least three amino acid in a row. (Table 2) Weekly similar molecular properties were able
to be found having 3 amino acids in a row as well, which indicate that their molecular functions
were less likely to be linked. ( Table 4). And lastly, there were very few dissimilar amino acid
chain due to the fact that these two organisms are closely related to each other. Although that, we
were able to find 2 amino acids in a row ( Table 4).
Questions
1. FIND IDENTICAL AMINO ACIDS
Can you find anywhere in the alignment where 2 amino acids in a row are identical? What are
the amino acids and their corresponding numbers? Yes.
Table 1.
Huynh 3
Species
Identical Amino Acid
Sequence
Numbers
Clostridium tetani
664-666
SFG or SerinePhenylalanine- Glycine
Clostridium butyricum
664-666
SFG or SerinePhenylalanine- Glycine
2. FIND STRONGLY SIMILAR AMINO ACIDS
Can you find anywhere in the alignment where 2 amino acids in a row are
strongly similar? What are the amino acids and their corresponding numbers? Construct a table
of your findings. Yes
Table 2.
Species
Strongly Similar Amino
Sequence
Acid Numbers (:)
Clostridium tetani
618-670
TKD or Threonine- LysineAspartic Acid
Clostridium butyricum
618-670
SRE or Serine- ArginineGlutamic Acid
Huynh 4
3. FIND WEAKLY SIMILAR AMINO ACIDS
Can you find anywhere in the alignment where 2 amino acids in a row are
weakly similar? What are the amino acids and their corresponding numbers? Construct a table of
your findings. Yes
Table 3.
Species
Weakly Similar Amino Acid Sequence
Numbers (.)
Clostridium tetani
361-363
FNK or PhenylalaineAsparagine- Lysine
Clostridium butyricum
361-363
FTT or Phenylalanine-
4. FIND DISSIMILAR AMINO ACIDS
Can you find anywhere in the alignment where 2 amino acids in a row are different and not
similar (not alike at all)? What are the amino acids and their corresponding numbers? Construct a
table of your findings. Yes
Table 4.
Species
Dissimiliar Amino Acid
Numbers
Sequence
Huynh 5
Clostridium tetani
253-254
KI or Lysine-Isoleucine
Clostridium butyricum
253-254
SK or Serine- Lysine
5. WHICH END (N- TERMINUS OR C-ERMINUS) OF THE DNA
TOPOISOMERASES IS THE MOST SIMILAR BETWEEN THE 2 DNA
TOPOISOMERASES? HOW DO YOU KNOW?
N-Terminus of these two DNA Topoisomerases is the most similar because N-Terminus side has
longer sequences of identical amino acids than the C-Terminus.
6. Of the 9 total DNA topoisomerase sequences, which 2 are the most homologous (most alike).
HOW DO YOU KNOW?
Clostridium tetani and Clostridium butyricum are the most homologous (most alike) to each
other because of their alignment scores, which indicate the similarity of those two DNA
topoisomerases. C. Tetani has score of 0.13373 and C. Butyricum has score of 0.13646 and their
difference are only 0.0027 which the smallest difference compared to the rest of DNA
topoisomerases.