Template:CAARD Alignment

Description

There are two methods of ancestral reconstruction - Joint and Marginal. In this section, we provide a multiple alignment including both input peptidases and ancestral ML sequences reconstructed using the Joint method.The alignment is available in several formats clicking below the option "Set 1". To build HMM profiles and MRC sequences we removed non-informative amino acid stretches and gaps from several ancestral ML reconstruction analyses You can also retrieve the processed Jrof output, clicking below the option "Set 2". Note however that should you cannot select option 2 is because the output was not processed.

Comments

Alignment obtained using CLUSTAL X (Thompson et al. 1997) and GENEDOC editor (Nicholas and Nicholas 1997) for manual refinement.

Groups of similarity

1= [E,Q] 	Glutamate and Glutamine.
2= [D,N]	Aspartate and Asparagine.
3= [G,P]	Amino acids frequent in β-turns
4= [S,T]	Small nucleophile amino acids.
5= [K,R,H]	Basic amino acids
6= [F,Y,W]	Aromatic amino acids
7= [Q,E,D,N]	Acidic amino acids and relatives
8= [L,I,V,M,A]	Aliphatic amino acids
9= [L,I,V,M,G,P,A,F,Y,W] 	Hydrophobic and aliphatic amino acids

Shaded

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Fasta

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PIR

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Philyp

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MSF

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Clustal

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Stokholm

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