MARGARITA VOROBEVA

As it can be seen from Table 1 and Table 2 below, homologous proteins such as ATP synthase epsilon chain or Chemotaxis protein CheA have at least 50% similarity in both local and global alignments. The last protein, however, shows only 30% similarity. Possible explanation is that FeS cluster assembly protein SufD complex contributes to the assembly or repair of oxygen-labile iron-sulfur clusters under oxidative stress. May facilitate iron uptake from extracellular iron chelators under iron limitation. Considering that E.coli is an anaerobic bacterium, the low procent of similarity may suggest that expressing genes evolved independently.

Global Alignment of homologous proteins

Table 1. Results of global alignment

Protein Name	ID 1	ID 2	Score	% Identity	% Similarity	Gaps	Indels
ATP synthase epsilon chain	ATPE_ECOLI	ATPE_BACSU	213,0	30,9	55,4	7	3
Chemotaxis protein CheA	CHEA_ECOLI	CHEA_BACSU	1042,5	33,9	56,5	68	14
FeS cluster assembly protein SufD	SUFD_ECOLI	SUFD_BACSU	233,5	21,7	37,9	154	21

Local Alignment of homologous proteins

Table 2. Results of local alignment

Protein Name	ID 1	ID 2	Score	% Identity	% Similarity	Gaps	Indels	Coverage 1, %	Coverage 2, %
ATP synthase epsilon chain	ATPE_ECOLI	ATPE_BACSU	220,0	33,6	60,2	1	1	92,08	96,21
Chemotaxis protein CheA	CHEA_ECOLI	CHEA_BACSU	1046,5	34,7	57,9	54	12	97,55	99,7
FeS cluster assembly protein SufD	SUFD_ECOLI	SUFD_BACSU	233,5	21,7	37,9	154	21	93,85	99,08

As it can be seen from Table 3 and Table 4 below, non-homologous proteins have only 6.7% of similarity global alignment and 38.7% in local alignment. The low similarity in global alignment is connected with the length of proteins (ADHE_ECOLI is almost 7 times longer than GS13_BACSU).

Global Alignment of non-homologous proteins

Table 3. Results of global alignment

Protein Name	ID	Score	% Identity	% Similarity	Gaps	Indels
General stress protein 13	GS13_BACSU	28,0	4,2	6,7	733	24
Aldehyde-alcohol dehydrogenase	ADHE_ECOLI

Local Alignment of non-homologous proteins

Table 4. Results of local alignment

Protein Name	ID	Score	% Identity	% Similarity	Gaps	Indels	Coverage, %
General stress protein 13	GS13_BACSU	41,5	22,6	38,7	43	7	77,69
Aldehyde-alcohol dehydrogenase	ADHE_ECOLI						14,59

The amount of possible homologous proteins is 731.It was observed that the alignment had been pretty decent. There also are some places where the conservativity reaches its maximum (total amount is 12). Proteins ATPE_BORPE and ATPE_BURM1 are quite identical so they may be homologous (needle test showed 76,6% similarity)