Protein motifs. PSSM and patterns. Prosite.

Task 1

Chosen AC: O05886
Protein: Ribosome hibernation promotion factor, or HPF
Functions: Neccessary for dimerization of active 70S ribosomes into 100S ribosomes in stationary phase (small ribosome subunit binding)
Organism: Mycobacterium tuberculosis (strain ATCC 25618 / H37Rv)

PSI-BLAST Iterations Table (Threshold = 0.001)

#	Amount of sequences producing significant alignments with E-value higher than 0,005	ID of a sequence producing the best alignment with E-value WORSE than threshold	E-value	ID of a sequence producing the worst alignment with E-value BETTER than threshold	E-value
1	31	P26983.1	0.001	P28613.2	6e-04
2	46	P9WMA8.1	0.009	P71346.3	5e-11
3	51	P9WMA8.1	0.002	P24694.1	2e-23
4	51	P9WMA8.1	0.002	P24694.1	5e-24
5	53	P9WMA8.1	0.001	P24694.1	4e-24
6	53	P9WMA8.1	0.001	P24694.1	5e-24
Next iterations had the same amount of sequences.

From the table above we can observe quite low E-value; most found proteins have the same ot almost the same function as the default protein; However, P9WMA8.1 is an another Mycobacterium tuberculosis protein, required in translation, so it has a different function.

Task 2

Family: Enolase
Organism: Escherichia coli (strain K12)
Consensus pattern (red frame on the picture below): [LIVTMS]-[LIVP]-[LIV]-[KQ]-x-[ND]-Q-[INV]-[GA]-[ST]-[LIVM]-[STL]-[DERKAQG]-[STA]

Changed pattern (black frame on the picture above): N-S-I-L-I-K-[FV]-N-Q-I-G-[ST]-L-T-E-T

Then, using PROSITE, I scanned my changed pattern and found 296 hits. In Uniprot list there are, however, 396 hits.
File with my hits: pattern.txt
Uniprot file: true.txt

To find all differences between those two lists, the Python script was created and all results were written down in the table below:

TP (True Positives - presented in both lists)	148
FP (False Positives - not presented in Uniprot list)	148
FN (False Negatives - hits from Uniprot list which weren't found in my list from PROSITE)	248

Table 2. Discovered differences

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