Table 1. Global pair alignment

Name	ID1	ID2	Score	% Identity	% Similarity	Gaps	Indels
Xylose isomerase	XYLA_ECOLI	XYLA_BACSU	1187.0	50.1%	66.2%	9	1
Signal recognition particle protein	SRP54_ECOLI	SRP54_BACSU	1203.0	51.6%	70.1%	23	4
Tryptophan synthase beta chain	TRPB_ECOLI	TRPB_BACSU	1098.5	53.4%	69.5%	23	8
Tryptophan synthase alpha chain	TRPA_ECOLI	TRPA_BACSU	340.5	30.2%	46.9%	41	7

Table 2. Local pair alignment

Protein Name	ID 1	ID 2	Score	% Identity	% Similarity	Gaps	Indels	Coverage 1	Coverage 2
Xylose isomerase	XYLA_ECOLI	XYLA_BACSU	1195.0	51.4%	67.9%	2	2	99.1%	97.5%
Signal recognition particle protein	SRP54_ECOLI	SRP54_BACSU	1205.0	54.0%	73.3%	8	2	97.7%	98.2%
Tryptophan synthase beta chain	TRPB_ECOLI	TRPB_BACSU	1102.0	55.2%	71.4%	13	5	97.2%	97.8%
Tryptophan synthase alpha chain	TRPA_ECOLI	TRPA_BACSU	348.0	35.5%	54.4%	2	2	85.1%	84.6%

Table 3. Proteins with different mnemonics using needle

Proteins' names	ID1	ID2	Score	Identity	Similarity	Gaps	Indels
Chromosomal replication initiator protein DnaA, 3-ketoacyl-CoA thiolase FadA	DNAA_ECOLI	FADA_ECOLI	28.5	11.8%	20.5%	346	24

Table 4. Proteins with different mnemonics using water

Proteins' names	ID1	ID2	Score	Identity	Similarity	Gaps	Indels	Coverage 1	Coverage 2
Chromosomal replication initiator protein DnaA, 3-ketoacyl-CoA thiolase FadA	DNAA_ECOLI	FADA_ECOLI	55.5	18.4%	34.9%	71	11	49.0%	57.4%

Some comments to Table 3 and Table 4

Alignments' characteristics you can look into the Tables (3, 4). Proteins are not homologous (there're only 11.8% Identity and 20.5 Similarity). Full coverage percentage is 49.0% and 57.4%. They're just "random proteins in our sample"

All proteins using needle

Pair alignment (project)

Protein's full names

Multiple alignment of proteins

Mnemonics: XYLA The total number of proteins: 225 Mostly proteins aligned good. The Organisms are: Arthrobacter sp, Streptomyces albus G, Actinoplanes sp, Arabidopsis thaliana and Lactobacillus pentosus. All of the except A. thaliana are Bacteria. So, tere're some differences in the sequence's lenghth. I guess, they're homological: we can notice any constant sequences'clusters (for example, WGGREG: 230 - 235). Also, we can image evolutionary tree (using Jmol) - we can follow to this evoltion changes. As you can see, A. thaliana's sequence is more different from other representatives.

---

© Belyaeva Julia, 2018