Practise 9. Aligning sequences

1. Global pairwise alignment of homologous proteins

Protein Name	ID1	ID2	Score	% Identity	% Similarity	Gaps	Indels
6-phosphogluconate dehydrogenase, NADP(+)-dependent, decarboxylating	6PGD_ECOLI	6PGD_BACSU	1718.0	70.0%	83.4%	3	3
Aspartate-semialdehyde dehydrogenase	DHAS_ECOLI	DHAS_BACSU	246.5	26.2%	45.2%	65	19
uvrABC system protein B	UVRB_ECOLI	UVRB_BACSU	2048.5	58.5%	77.7%	12	4

2. Local pairwise alignment of homologous proteins

Protein Name	ID1	ID2	Score	% Identity	% Similarity	Gaps	Indels	Coverage 1	Coverage 2
6-phosphogluconate dehydrogenase, NADP(+)-dependent, decarboxylating	6PGD_ECOLI	6PGD_BACSU	1719.0	70.1%	83.6%	3	3	99.79%	99.79%
Aspartate-semialdehyde dehydrogenase	DHAS_ECOLI	DHAS_BACSU	257.5	26.8%	46.2%	64	15	98.09%	97.69%
uvrABC system protein B	UVRB_ECOLI	UVRB_BACSU	2055.5	59.2%	78.5%	8	3	98.96%	99.55%

3. The result of applying alignment programs to unrelated proteins

Alignment type	ID1	ID2	Score	% Identity	% Similarity	Gaps	Indels	Coverage 1	Coverage 2
Global	UVRB_ECOLI	DHAS_BACSU	49.0	5.4%	11.4%	623	11	-	-
Local	UVRB_ECOLI	DHAS_BACSU	56.0	16.5%	35.2%	75	9	33.43%	35.4%

4. Multiple Protein Alignment and Import into Jalview

The query "mnemonic:uvrb_*" was used to search for proteins with the function mnemonic "UVRB".

Total finds:382, of which in Swiss-prot:377

The following proteins were chosen:

UVRB_RHOBA

UVRB_MYCGE

UVRB_XANOP

UVRB_EDWI9

UVRB_HALMA

Recommended full name (Ecoli): UvrABC system protein B

Multiple alignment was done with Jalview, the result is this project:

Multiple Alignment

The sequences have aligned very well. They fully overlap in the following areas: 19,21,27,29-32,34-35 38, 45, 49, 51-53, 55-56, 58-60,62, 74, 80-84, 86-87, 90, 95-96, 98-100, 102-103, 105-106, 108, 110-115, 123, 125, 130, 133, 137, 147, 149, 156, 159-160, 165, 195, 198, 205, 207-208, 211, 218, 227, 259, 273, 281, 298-299, 304, 307, 315, 317, 319, 321-323, 327, 336, 341, 351-355, 357, 359-360, 368, 371-372, 375, 379-383, 385, 387-391, 393, 395, 406-410, 414, 428-430, 432, 434-435, 445, 449, 462, 465-466, 468-469, 474, 476, 479, 482, 491, 498-499, 506-507, 509, 514-516, 518-525, 527-529, 531-532, 534, 536-538, 541, 544, 549, 551, 554-559, 578-579, 581, 584, 586, 589, 593, 596, 600, 659, 663, 669, 671, 675-676, 651. Plots of smallest homology: 1-19, 606-654, 682-730. I think that all the selected proteins are homologous.