OBJECTIVES

1. To be able to retrieve protein sequence for heat shock protein DNA jc12
2. To explore how raw sequence data is scrutinized in order to extract biological
meaning from it
3. To explore ways of searching for homologs

INTRODUCTION

Bioinformatics is the study of information content and information flow in biological systems
and processes. Bioinformatics makes use of computers to conduct the analysis of sequence in
a fraction of seconds. It serves as the bridge between observations (data) in diverse
biologically-related discipline and the derivations of understanding (information) about how
the systems or processes function and subsequently the application (knowledge).
Bioinformatics involves collection, storage, retrieval and analysis of biological data that has a
lot of applications in pharmaceutical, agricultural and food industries, and in molecular
genetics research (Arda et al, 2003)

Biological data are generated from various genome sequencing projects, obtained by
different techniques like ONA sequencing (genome and EST), 2D gel electrophoresis, mass
spectroscopy and molecular markers. The national centre for biotechnology information
(NCBI) is located in Bethesda, Maryland was founded in 1988 through legislation sponsored
by Senator Claude Pepper. The NCBI houses are series of database relevant to biotechnology
and biomedicine and is an important resource for bioinformatics tools and services. Major
databases include GenBank for DNA sequences and PubMed, a bibliographic database for the
biomedical literature. Other databases include the NCBI Epigenomics database. All these
database are available online through the Entrez search engine. Comamonas testosteroni is a
gram-negative soil bacterium. Strain i2 gfp has been used in bioaugmentation trials, in
attempts to treat the industrial byproduct 3-chloroniline (Roca, 1995)
MATERIAL

Computer

Protein DNA jc 12(Comamonas testosteroni)

METHODS

An internet browser was launched. NCBI address was typed in address bar and the NCBI
website was opened. On the NCBI website the protein site were selected and DNA jc12 was
typed on search bar and search for results. Protein results was selected and the FASTA format
was chosen. Then the sequence comes out showing protein names and additional analysis.
The BLAST was ran in FASTA sequence and algorithm for BLAST use were selected. After
blast was completed, a graphic summary were displayed showing putative domains and
alignments sequences.
QUESTIONS

1. https://blast.ncbi.nlm.nih.gov/blast.cgi?PAGE=proteins

- https://www.ncbi.nlm.nih.gov/trm=DNA+jc12

2. WP 034358983.1 length 898

WP 012837599.1

WP 034407620.1

WP 054075788.1

3. Accession number is a unique identifier given to a DNA or protein sequence record to

allow for tracking of different versions of that sequence record and the associated sequence
over time in a single data repository.

4. comamonas testosteroni

5. Methionine

6. (a) Glycine

(b) -Glutamine

(c) -Leucine

(c) -Alanine

(d) -Threonine

7. It shows the sequence of DNA, RNA, or protein to identify regions of similarity that may
be consequence of structural relationships between the sequences.

8. DNA gyrase subunit A [comamonas aquatica]

DNA gyrase subunit A [comamonas terrigena]

DNA gyrase subunit A [Delftia tsuruhatensis]

 DNA gyrase subunit A [Delftia acidovorans]

9. T cell receptor beta chain[Homo sapiens]

T cell receptor beta chain CDR3[Homo sapiens]

T cell receptor beta chain V-D-J-region[Homo sapiens]

REFERENCES

1. Roca j, Trends Biochem Sci, 1995, vol. 5 (pg 39-47)

2. Arda B, Aydemir S & Serter, D (2003). Comamonas testosteroni meningitis in a

patient with recurrent cholesteatoma. APMIS 111, 474-476

3. Horinouchi, M., Yamamoto, T., Taguchi, K., Arai, H & Kudo, T. (2001). Meta-
cleavage enzyme gene tesB is necessary for testosterone degradation in comamonas
testosteroni TA441. Microbiology 147, 3367-3375
 UNIVERSITY OF VENDA

SCHOOL OF MATHEMATICAL AND NATURAL SCIENCES

DEPARTMENT OF BIOCHEMISTRY

Name : MADZIVHANDILA L

Student no : 14009226

Date : 27 FEBRUARY 2017

Assessment : PRACTICAL 1

Module code : BCM 3521

Title
Bioinformatics
DISCUSSION

Comamonas testosterone is a gram positive bacterium. Strain 12 gfp has been used in bio
augmentation trials.

Figure 2 is showing FASTA format of Comamonas testosteroni, which is text based format
for representing peptide sequence in which amino acids are represented using single letter
codes. The FASTA format shows the GenBank number which is KGH10346.1, the
arrangement of amino acids which starts with methionine

Figure 3 shows BLAST graphic summary of Comamonas testosteroni. The numbered blue
bar at the top represent the query sequence. Database hits are shown aligned to the query
below the numbered bar of the aligned sequence, the most similar are shown closest to the
query.

Figure 4 is showing the BLAST description format of Comamonas testosteroni. Each line is
composed of the GI number, database designation, accession number and locus name for the
matched sequence, separated by vertical bars. According to protein Comamonas testosterone
the number of protein that have identities greater than 95% is twelve.

Figure 5 shows the BLAST alignment format of Comamonas testosteroni. The alignment is
precede by the sequence identifier, the full definition line and the length of the matched
sequence in amino acids and then the bit score. The line between the two sequences indicate
the similarities between the two sequences.

CONCLUSION

Bioinformatics is the best computer software that is used to analyse and integrate biological
information. Protein sequencing play a major role in determining the amino acids present and
their homologs relationship is given protein.