Bioinformatic Using Diferent Technique Essay

569 words - 3 pages

Summary feedback on key issues
Assessor:
Grade:
You have identified your enzyme and its properties correctly / partly correctly / incorrectly.
Your investigations and searches are complete / mostly complete / incomplete.
You have provided extensive / adequate / inadequate supporting information.
Your report demonstrates good / satisfactory / partial / inadequate understanding of the web site outputs.
Other comments:

Bioinformatics Report

Sequence file number: Seq09 Seq09 .txt

1. Results from BLASTn search (giving only one example of multiple matches to the same sequence from the same species/strain under different accessions, i,e whole genome, isolated gene, cDNA):
GenBank ID Description Score Frequency (E) value
XM_003314320.2
PREDICTED: Pan troglodytes phosphorylase 488 8e-135
XM_003314319.2
PREDICTED: Pan troglodytes phosphorylase 488 8e-135
XM_001145433.3
PREDICTED: Pan troglodytes phosphorylase 488 8e-135
XM_003831725.1
...view middle of the document...

/ Kyte & Doolittle, the individual values for the 20 amino acids are:
Ala: 1.800 Arg: -4.500 Asn: -3.500 Asp: -3.500 Cys: 2.500 Gln: -3.500
Glu: -3.500 Gly: -0.400 His: -3.200 Ile: 4.500 Leu: 3.800 Lys: -3.900
Met: 1.900 Phe: 2.800 Pro: -1.600 Ser: -0.800 Thr: -0.700 Trp: -0.900
Tyr: -1.300 Val: 4.200 : -3.500 : -3.500 : -0.490
________________________________________
Weights for window positions 1,..,9, using linear weight variation model:
1 2 3 4 5 6 7 8 9
1.00 1.00 1.00 1.00 1.00 1.00 1.00 1.00 1.00
edge center edge
________________________________________

4. Protein similarity (blastp) search results (selecting only one match per species):

UniProt Code Protein name Species Score Frequency (E value) Identities positives
AAC17450.1
liver glycogen phosphorylase Homo sapiens 1760
0 99% 99%
JAA39156.1
phosphorylase Pan troglodytes 1754
0 99% 99%
XP_003901831.1
glycogen phosphorylase Papio anubis 1750
0 99% 99%
XP_002824778.1
glycogen phosphorylase Pongo abelii 1750
0 99% 99%
XP_003267721.1
glycogen phosphorylase Nomascus leucogenys 1749
0 99% 99%
XP_001102253.1
glycogen phosphorylase Macaca mulatta 1744
XP_002753938.1
glycogen phosphorylase Callithrix jacchus 1677
95% 95%
XP_003930581.1
glycogen phosphorylase Saimiri boliviensis boliviensis
1675
98% 98%
XP_003792196.1
glycogen phosphorylase Canis lupus familiaris 1649
95% 95%
EHB10195.1
glycogen phosphorylase Heterocephalus glabe 1643 99% 95%

5. Protein structure

a. Protein domains, motifs etc. Enter brief details of any information found:

b. Secondary structure prediction
What are the predicted percentages of:

Helix - 50.53%

 Sheet - 11.92%

 turn - 6.02%

Random coil - 31.52%
6. 3D structure
Relevant PDB filename: .pdb
3DD1
Crystal structure of glycogen phophorylase complexed with an anthranilimide based inhibitor GSK254


a. Attach an image of the 3D structure (using a related organism if you cannot find a structure for the protein corresponding to your gene).

b. Is the predicted secondary structure content similar to that seen in the observed structure?

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