between Bos taurus - Canis lupus, Homo sapiens - Bos Taurus, Bos taurus - Danio rerio, and
Canis lupus - Danio rerio; ■ a good similarity on α2 chain exists between Bos taurus - Canis
lupus, Homo sapiens - Canis lupus, and Homo sapiens - Bos taurus.
Table 3.
Collagen chains similarity matrix (expressed as percent)
|
BT α1 |
BT α2 |
CL α1 |
CL α2 |
DR α1 |
DR α2 |
HS α1 |
HS α2 |
RN α1 | |
|
BT_a1 = Bos taurus CTIα1 |
100 | ||||||||
|
BT_a2 = Bos taurus CTIα2 |
47.19 |
100 | |||||||
|
CL_a1 = Canis lupus CTIα1 |
97.43 |
47.38 |
100 | ||||||
|
CL_a2 = Canis lupus CTIα2 |
48.71 |
94.51 |
50.18 |
100 | |||||
|
DR_a1 = Danio rerio CTIα1 |
75.74 |
49.38 |
76.37 |
47.00 |
100 | ||||
|
DR_a2 = Danio rerio CTIα2 |
42.77 |
60.16 |
43.46 |
58.13 |
36.73 |
100 | |||
|
HS_a1 = Homo sapiens CTIα1 |
82.39 |
35.35 |
82.56 |
34.58 |
62.56 |
38.08 |
100 | ||
|
HS_a2 = Homo sapiens CTI α2 |
53.23 |
93.33 |
52.09 |
94.51 |
49.41 |
66.15 |
40.49 |
100 | |
|
RN_a1 = Rattus norvegicus CTIα1 |
72.79 |
20.93 |
72.32 |
20.58 |
44.22 |
22.11 |
74.05 |
9.34 |
100 |
|
RN_a2= Rattus norvegicus CTI α2 |
18.64 |
70.63 |
14.00 |
66.56 |
25.80 |
40.62 |
15.18 |
66.97 |
38.94 |
Table 4.
Collagen chains Levenshtein distances within and between species
|
BT α1 |
BT α2 |
CL α1 |
CL α2 |
DR α1 |
DR α2 |
HS α1 |
HS α2 |
RN α1 | |
|
BT α1 |
_____0 | ||||||||
|
BT α2 |
903 |
~~0 | |||||||
|
CL α1 |
____70 |
892 |
_____0 | ||||||
|
CL α2 |
893 |
____98 |
891 |
_____0 | |||||
|
DR α1 |
469 |
902 |
440 |
896 |
______0 | ||||
|
DR α2 |
909 |
463 |
903 |
492 |
909 |
~~0 | |||
|
HS_a1 |
429 |
882 |
448 |
883 |
731 |
871 |
_____0 | ||
|
HS α2 |
884 |
115 |
883 |
____76 |
895 |
487 |
874 |
_____0 | |
|
RN α1 |
1031 |
921 |
1033 |
921 |
1016 |
890 |
650 |
923 |
______0 |
|
RN α2 |
1061 |
941 |
1059 |
944 |
1044 |
923 |
671 |
940 |
428 |
The Levenshtein distances, defined as the minimal numbers of characters that must be
replace, insert or delete to transform one chain into other are presented in Table 4. With
seventy amino acids characters replace, insert or delete the α1 collagen type I chain of Bos
taurus could be transformed in α1 collagen type I chain of Canis lupus. With ninety-eight
amino acids characters replace, insert or delete the α2 collagen type I chain of Bos taurus
could be transformed in α2 collagen type I chain of Canis lupus. The greater dissimilarity was
identified when collagen type I chains of Rattus norvegicus are compared with other species
(see Table 3 and 4). This could be explained by the existence of a great number of unknown
or unidentified amino acids and/or by the absence of the cysteine and tryptophan (see Table
1).
CONCLUSIONS
The scale of amino acids hydrophobic or hydrophilic is still on debate even if there
were proposed many methods. The scale proposed by Welling et al. seems to be more stable
on principal component analysis on investigated scales.
The similarity analysis revealed that there are good similarities on Collagen type I
amino acids chains between Bos Taurus and Canis lupus, as well as between Bos Taurus and
Homo sapiens. Due to the lack of amino acids identification on collagen type I of Rattus
norvegicus the greatest dissimilarities were observed when this specie was compared with the
other analyzed species.
314
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