ALIGNMENTS

Alignments

Similar mnemonics

Characteristics of global pairwise alignments for 3 protein pairs (needle)

Protein name	ID 1	ID 2	Score	% Identity	% Similarity	Gaps	Indels
Ribose import ATP-binding protein RbsA	RBSA_ECOLI	RBSA_BACSU	1129.0	46.2%	64.7%	10	4
Protein RecA	RECA_ECOLI	RECA_BACSU	1069.5	56.9%	75.7%	23	5
Ribonucleoside-diphosphate reductase 1 subunit alpha	RIR1_ECOLI	RIR1_BACSU	465.0	21.3%	36.7%	233	32

Characteristics of local pairwise alignments for 3 protein pairs (water)

Protein name	ID 1	ID 2	Score	% Identity	% Similarity	Gaps	Indels	Coverage E.coli	Coverage B.subtilis
Ribose import ATP-binding protein RbsA	RBSA_ECOLI	RBSA_BACSU	1136.0	47.3%	66.3%	2	2	97,6%	99,2%
Protein RecA	RECA_ECOLI	RECA_BACSU	1072.5	58.5%	77.8%	16	3	98,3%	97,9%
Ribonucleoside-diphosphate reductase 1 subunit alpha	RIR1_ECOLI	RIR1_BACSU	475.0	23.5%	40.9%	148	28	85,8%	96,7%

Ribonucleoside-diphosphate reductase subunit alpha protein from Bacillus subtilis is inferred from homology, which may causes on a results of a study.

Different mnemonics

Characteristics of global pairwise alignments for proteins with different mnemonics (needle)

Protein name	ID 1	ID 2	Score	% Identity	% Similarity	Gaps	Indels
Formate-dependent phosphoribosylglycinamide formyltransferase (E.coli) and Menaquinol-cytochrome c reductase iron-sulfur subunit (B.subtilis)	PURT_ECOLI	QCRA_BACSU	16.0	6.6%	9.9%	349	8

Characteristics of local pairwise alignments for proteins with different mnemonics (water)

Protein name	ID 1	ID 2	Score	% Identity	% Similarity	Gaps	Indels	Coverage E.coli	Coverage B.subtilis
Formate-dependent phosphoribosylglycinamide formyltransferase (E.coli) and Menaquinol-cytochrome c reductase iron-sulfur subunit (B.subtilis)	PURT_ECOLI	QCRA_BACSU	36	20.5%	33.3%	56	8	33,1%	46,7%

Obvious calculations show that percentage of identity in the random pair of proteins should be 5% roughly. The experimental percentage is quite similar. A large number of gaps may be caused by differences in protein size (168AA/392AA). The percents of coverage in local alignment differ from the same one in proteins with equal mnemonics, which also quite reasonable.

Jalview import

Global alignment of RBSA_ECOLI and RBSA_BACSU proteins (Jalview project)

Multiple alignments

Global alignment of RbsA protein in different bacteria species

Multiple alignments were done successfully, conservative and non-conservative columns both are presented in the alignment. Each protein seems to be homological to others: the minimal score in pairwise alignments is 8940.0.

© Gumerov Ruslan, 2017