Task 2: Sequence alignments (sequence searches and multiple alignments)

Task description

The full description of this task can be found here.

Task 2.2: Multiple sequence alignments

Methodology

For each identity range (99%-90%, 89%-60, 59%-40% and 39%-20%) we selected five sequences of which at least one sequence has a solved structure as well. In order to find these sequences we looked in our blast and psi-blast results for appropriate sequences, four for each identity range. A sequences was considered as appropriate if it has the wanted sequence identity to our reference sequence and if this sequence has roughly the same length as our reference sequence. The reason for this is that we wanted to avoid leading and trailing gaps in our alignments. However, this was not always possible , especially for the low identity range (39%-20%). Last but not least, we used our hhsearch results (which was queried against a profile database of all pdb entries) to find appropriate sequences for each identity range. The list of selected sequences is as follows:

Sequence Identity	GI/PDB	Remark
97%	4557819	phenylalanine-4-hydroxylase [Homosapiens]
95%	1J8T	catalytic domain of human phenylalanine hydroxylase Fe(II)
94%	296212713	PREDICTED:phenylalanine-4-hydroxylase [Callithrix jacchus]
91%	296212713	PREDICTED:phenylalanine-4-hydroxylase-like [Ailuropodamelanoleuca]
90%	171543886	phenylalanine-4-hydroxylase [Musmusculus]
89%	126339754	PREDICTED: similar toPhenylalanine-4-hydroxylase (PAH) (Phe-4-monooxygenase)[Monodelphis domestica]
82%	224095451	PREDICTED: phenylalanine hydroxylase [Taeniopygia guttata]
73%	32442452	Pah [Danio rerio]
66%	3HF6	crystal structure of human tryptophan hydroxylase type 1 with bound LP-521834 and FE
60%	194865387	GG14450 [Drosophila erecta]