Choice of the best matrix and parameters for GDH sequences alignment The alignments are made using :

(1)

Choice of the best matrix and parameters for GDH sequences alignment

The alignments are made using : ClustalW at EBI (Cambridge)

Reference : Thompson, J. D., Higgins, D. G., & Gibson, T. J. (1994) "CLUSTAL W: improving the sensitivity of progressive multiple sequence alignment through sequence weighting, position-specific gap penalties and weight matrix choice" Nucleic Acids Res. 22, p 4673 - 4680

Example with the subset H :

GDH NOT EC classified Viridiplantae

length range [411 - 470]

Get the files (ZIP

compressed) in FASTA format : Subset H

matrix PAM BLOSUM GONNET Id

alignment score (default values for all

parameters) 25246 25366 25471 25487

parameter value score PAM score BLOSUM

score

GONNET score Id

"Gapopen"

(default = 10)

1 25818 26193 26243 26720

2 25783 25783 26044 26224

100 21890 22150 22636 22636

"Endgap" 10 25246 25366 25471 25487

20 25246 25366 25471 25487

"Gapext"

(default = 0,2)

0,05 25246 25366 25471 25487

0,5 25246 25366 25471 25487

5 25246 25366 25471 25471

10 25246 25366 25471 25471

Gapdist 10 25246 25366 25471 25487

(2)

(default = 4) 5 25246 25366 25471 25487

1 25246 25366 25471 25487

Matrix Gapopen Endgap Gapext Score

Gonnet default = 10 default = ? default = 0,05 33558

PAM default default default 33207

Gonnet 1 default default ³⁵⁵⁴⁵_score)^(Highest

PAM 1 default default 35003

Gonnet 1 10 default 35545

Gonnet 1 20 default 35545

Gonnet 1 default 0,05 35545

Gonnet 1 default 0,5 35511

Gonnet 1 default 5 35076

Gonnet default default 5 33298

Gonnet 1 default 10 34737

Gonnet 1 default 1 35503(Best

alignment)

Finally, "eye" inspection allows to choose the Gonnet matrix although the highest score is obtained with the Id matrix.

1. Id matrix : Gapopen = 1 - Other default values : SCORE = 26720

gi|15240793|ref|NP_196361.1| ILG-LDSKI----ERSLMI-PFREIKVECTIPKDDGTLVSYIGFRVQHDN 60 gi|15004984|dbj|BAB62170.1| ILG-LDSKI----EKSLMI-PFREIKVECTIPKDDGTLVSYVGFRVQHDN 60 gi|28269441|gb|AAO37984.1| LLG-LDSKL----EKSLLI-PFREIKVECTIPKDDGTLASYVGFRVQHDN 60 gi|7431768|pir||T16982 LLG-LDSKL----EQCLLI-PFREIKVECTIPKDDGSLATFIGFRVQHDN 60 gi|15054452|dbj|BAB62312.1| -LAVLD--LPPAMEK-IVITPQREMTVELIINRDDGKPESFMGYRVQHDN 94 gi|15054450|dbj|BAB62311.1| -LAVLD--LPPAMEK-IVITPQREMTVELIINRDDGKPESFMGYRVQHDN 94 *. ** : *: ::* * **:.** * :***. :::*:******

(3)

2. GONNET matrix : Gapopen = 1 - Other default values : SCORE = 26243

gi|15240793|ref|NP_196361.1| ILGLDSKIERSLMIPFREIKVECTIPKDDGTLVSYIGFRVQHDNARGPMK 66 gi|15004984|dbj|BAB62170.1| ILGLDSKIEKSLMIPFREIKVECTIPKDDGTLVSYVGFRVQHDNARGPMK 66 gi|28269441|gb|AAO37984.1| LLGLDSKLEKSLLIPFREIKVECTIPKDDGTLASYVGFRVQHDNARGPMK 66 gi|7431768|pir||T16982 LLGLDSKLEQCLLIPFREIKVECTIPKDDGSLATFIGFRVQHDNARGPMK 66 gi|15054452|dbj|BAB62312.1| VLDLPPAMEKIVITPQREMTVELIINRDDGKPESFMGYRVQHDNARGPFK 100 gi|15054450|dbj|BAB62311.1| VLDLPPAMEKIVITPQREMTVELIINRDDGKPESFMGYRVQHDNARGPFK 100 :*.* . :*: :: * **:.** * :***. :::*:**********:*