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STUDENT NAME

PROFESSOR NAME

DATE

Q1

1. Use the NCBI or EBI portals to retrieve one file for each of the several different forms of creatine kinase found in humans. Each file should contain the complete mRNA sequence.

ANSWER

Please check the sequence.txt output file from NCBI having coding sequence of 3 Different forms of creatine kinase found in humans.

That is mus musculus, hellcoverpa armlgera and aedes aegyti.

b. Compile a table, similar to the one from tutorial 1, comparing the sequence elements of the mRNA of each different creatine kinase forms that you find. Include extra columns indicating the length of the protein and the receptor sub-type.

Comment on your findings.

Open the files and check complete mRNA sequence and found 3 different accession number.

C.Retrieve files for two genes of the hexokinase types you retrieved in part (a) and compare the structure of the genes (exon/intron profile). Comment on your findings.

Using NCBI for the sequence of Mus musculus hexokinase (Hk-1) mRNA, complete cds, Helicoverpa armigera hexokinase (HK) mRNA, complete cds and Aedes aegypti hexokinase (HK) mRNA, complete cds and the fast sequence is shown above.

Qn2

The protein p53 acts as a tumour suppressor in many tumour types, inducing growth arrest or apoptosis depending on the physiological circumstances and cell type. It is involved in cell cycle regulation as a trans-activator that acts to negatively regulate cell division by controlling a set of genes required for this process.

In this question you will explore the relationship of the p53 sequence for several different species.

(i) Using UniProt locate the sequence for the full-length human sequence of the tumour repressor protein p53. Then do a BLAST run using this sequence at the NCBI site (blast.bcbi.nlm.nih.gov) searching against the Swiss-Prot protein database and identify the sequences of 7 other different species of the p53 protein (make sure they are full length sequences). Include in your answer a commentary of what you did and where, along with appropriate screenshots.

NCBI identify 7 different species such as Homo sapiens, Macaca mulatta, Macaca fascicularis, Canis lupus familiaris, Felis catus, Balaenoptera acutorostrata and Ovis aries.

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2. Give the Accession number for each protein sequence identified, together with the species. Give the percentage identity for each of the 7 sequences with that of the human sequence. State E values and the length of each sequence.

The percentage starting 100% and each species have different percentage.

The E values length is all 0.0. and the first 3 length of sequence are same.

3. For all 8 sequences run a multiple sequence alignment using program Clustal Omega and show the alignment generated.

The first of the 8 sequence is not fully complete some of the sequence is missing.

4. How many positions along the multiple sequence alignment are fully conserved en species?.

This multiple sequence are 6 sequence are fully protected species and the all have equal se length. Clustal Omega means practised to run Multiple Sequence Alignment Supports to identification from conserved sequence regions to a group of sequences Conserved regions are important functionally.

5. Display both the cladogram and phylogram trees obtained for the aligned sequences. Briefly discuss the evolutionary relationship between the 8 species as indicated by the phylogram and cladograms. Which species is the closest relation to the human species?

The closest relationship between human species of phylogenetics and cladogram is MOUSE, MACMU and MACFA.

Qn3

Detecting remote homologs with BLAST and PSI-BLAST.

The NCBI website

(http://www.ncbi.nlm.nih.gov)

Input blast

Discuss what you observe from the BLAST and PSI-BLAST searches. Discuss which of the two search methods proved most effective and why.Include output as appropriate to illustrate your answer, including the pairwise alignment for the two sequences generated from your work. First, the screenshot accession number is P00813, and E-values is low, and the percentage is high. The second screenshot is accession number P76641 E-value is very high, and the percentage is low PSI-Blast output.

gives the option to run both BLAST and PSI-BLAST for a query protein sequence. For this question you need to use the NCBI website to run both BLAST and PSI-BLAST.

Pairwise Alignments

The enzyme adenosine deaminase (UniProt accession number P00813) and the enzyme guanine deaminase (UniProt accession number P76641) perform a similar function and are remote homologs, both belonging to the SCOP superfamily metallo-dependent hydrolase. The two sequences have a percentage identity of only 15%.Using NCBI search against the UniProtKB/Swiss-Prot database, choosing the PSI-BLAST Algorithm.

The guanine deaminase P76641 repeated three-time ns iteration, to identify 15% guanine deaminase is not present homologues.The guanine deaminase P76641 repeated three-times iteration, to identify 15% guanine deaminase is not present homologues.

Using NCBI search against the UniProtKB/Swiss-Prot database, choosing the PSI-BLAST Algorithm.

The guanine deaminase P76641 repeated three-times iteration, to identify 15% guanine deaminase is not present homologues.

NCBI search engine for the Life Sciences The webpage gives each searchable databases open Introduces the protein sequence database Select the database the protein in this case,Output from BLAST/ PSI-BLAST

NCBI search engine for the Life Sciences The webpage gives each searchable databases open Introduces the protein sequence database Select the database the protein in this case,Output from BLAST/ PSI-BLAST

Output from BLAST/PSI-BLAST

Perform a protein-protein BLAST search using the sequence for the adenosine deaminase sequence (UniProt accession number P00813) searching against the UniProtKB/Swiss-Prot database. Search the results for the guanine deaminase enzyme (UniProt accession number P76641). Now repeat using PSI-BLAST and compare your results from those obtained from protein-protein BLAST.

Input blast

Discuss what you observe from the BLAST and PSI-BLAST searches. Discuss which of the two search methods proved most effective and why.Include output as appropriate to illustrate your answer, including the pairwise alignment for the two sequences generated from your work. First, the screenshot accession number is P00813, and E-values is low, and the percentage is high. The second screenshot is accession number P76641 E-value is very high, and the percentage is low PSI-Blast output.

d

Qn4

Use the two protein domain databases Pfam and SMART to investigate the domain structure of the protein human Matrix metalloproteinase-15 (accession code P51511). Discuss the domains located within the sequence using the two different databases and compare and contrast the results found. Include a commentary of what did at each database with screenshots appropriate. Briefly discuss the functional role of the different domains located.

Pfam is a large number of multiple sequence alignments. Pfam for Accession number P051511. Domain of the PSI integrin starting 25 end 76, Domain of the integrin_beta start 138 end 382, Domain I-EGF_1 start 466 end 495, Domain EGF 2 start 599 end 630, Domain integrin B tail 640 end 728 and Domain integrin b cyt start 752 end 796.For P05556 the are7domains:PSI domain – from amino acid 26-76, and INB domain – from amino acid 34-464,VWA domain – from amino acid 142-372, domain – from amino acid EGF_like 559-591, domain – from amino acid Integrin_B_tail 640-728 and domain – from amino acid Integrin_b_cyt 752-798.

Reference

Known post-translational modifications of human Spl and Sp3 and the amino acid residues modified

(http://www.uniprot.org/uniprot/POB047 http://www.phosphosite.o g: http://www.uniprot.org/uniprot/Q02447; Chu and Ferro 2005 Chuang et al. 2008. Wei et al., 2009)

http://www.ncbi.nlm.nih.gov/bioproject/PRINA392950/ ..https://www.ncbi.nlm.nih.gov/bioproject/PRINA378930/.. The role of reticulation in the rapid diversification of organisms is attracting greater attention in evolutionary biology: Here, we report a population genomics approach to test the role of

Phylogenetic tree of representative orthologs of SR-BI from different species Amino acid sequences from the various SR. BI orthologs were analyzed using the multiple sequence alignment program Clustal Omega from EMBL-EB: http://www.ebi.ac.uk/Tools/msa/clustalo) Structural features of