Protein seqences alignments

Table 1. Global homologic seqences alignments

Protein name	ID1	ID2	Score	% Identity	% Similarity	Gaps	Indels
ATP-dependent Clp protease proteolytic subunit	CLPP_BACSU	CLPP_ECOLI	694.0	63.8%	77.6%	16	2
RNA polymerase-associated protein RapA(*)	RAPA_BACSU	RAPA_ECOLI	43.0	9.6%	15.6%	730	26
Cysteine--tRNA ligase	SYC_BACSU	SYC_ECOLI	1068.5	44.4%	60.3%	29	5

(*) Response regulator aspartate phosphatase A (in Bacillus subtilis)

Table 2. Local homologic seqences alignments

Protein name	ID1	ID2	Score	% Identity	% Similarity	Gaps	Indels	Coverage 1	Coverage 2
ATP-dependent Clp protease proteolytic subunit	CLPP_BACSU	CLPP_ECOLI	695.0	69.8%	84.9%	0	0	97.5%	92.8%
RNA polymerase-associated protein RapA(*)	RAPA_BACSU	RAPA_ECOLI	54.5	19.3%	31.3%	192	27	87.8%	46.3%
Cysteine--tRNA ligase	SYC_BACSU	SYC_ECOLI	1071.5	44.7%	60.8%	27	4	99.1%	99.6%

(*) Response regulator aspartate phosphatase A (in Bacillus subtilis)

Table 3. Non-homologic seqences alignments

	ID1	ID2	Score	% Identity	% Similarity	Gaps	Indels
Global	CLPP_BACSU	SYC_ECOLI	33.0	9.3%	15.1%	334	10
Local	CLPP_BACSU	SYC_ECOLI	58.0	21.4%	37.6%	54	9

Non-homologic seqences alignments have a significantly lower score and identity percentage than the homologic ones, as expected. In the local alignment most of the seqences are left out. However, none of the values is zero for non-homologic seqences.

Global alignment of CLPP_BACSU and CLPP_ECOLI in a Jalview project.

Multiple alignment of 5 CLPP proteins in a Jalview project. Across these proteins there are several conservative sights around the same spot, so they are probably homologic. However, the protein from Chlamydomonas moewusii is significantly longer than the others.