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.