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Topic B6db families

Families of PLP-dependent enzymes


Families of PLP-dependent proteins are defined as monophyletic groups of sequences possessing the same enzymatic function.


In assembling the B6 DataBase, whenever a given PLP-dependent activity could be associated to known sequences we proceeded to create one or more families corresponding to that activity. A first step in the creation of enzyme families was thus the careful examination of the literature, that provided a collection of functionally validated sequences (for such validated proteins, ID tags are shown in bold).
The number of sequences in individual families was then increased by homology searches, i.e. by scanning the GenBank with BLAST or by psi-BLAST.
Subsequently, Hidden Markov models (HMMs) were built from family alignments and incorporated in the database. These HMMs can be used for the functional classification of PLP-dependent enzymes in genomic sets of predicted protein sequences

When performing BLAST or psi-BLAST, criteria for inclusion of a (non-functionally validated) sequence in a family were the following:
(1) Only sequences yielding an e score <10-10 were generally considered (this limit could be somewhat lowered for families composed of short sequences).
(2) Sequences showing a >95% identity to a functionally verified protein were usually discarded, to diminish redundancy.
(3) Sequences being substantially (>30%) shorter than the shortest functionally verified protein were discarded. Sequences lacking the catalytic lysine residue were also discarded (except for rare cases in which the protein is known not to bind the cofactor via a lysine).
(4) Sequences showing a higher similarity to other characterized PLP-dependent enzymes (i.e., to some functionally verified protein belonging to another family) were discarded.
(5) Finally, sequences from taxa in which the enzymatic activity of the family was not documented, were also generally discarded.

Usage notes

Functionally validated sequences in a particular protein family are shown in bold.

last changed 2009/01/09 13:13

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