Based on sequence similarities, it was not possible to predict unambiguously the nucleophile catalyst.
Enumerating all families and establishing family membership consistently based on sequence similarities are nontrivial computational problems.
Next, we predicted multicopper oxidase-encoding genes based on sequence similarities, and full-length multicopper oxidase-encoding genes were curated using the GeneWise algorithm.
In Arabidopsis enzymes capable of activating fatty acids belong to a superfamily of acyl-activating enzymes (AAEs), which consists of 63 members, and is divided into seven clades based on sequence similarities (Shockey et al. 2003).
Based on sequence similarities among putative TPx's derived from various cyanobacteria genomes, we designated the seven putative TPx members as VCP, VCT, TCS, and GCT clusters according to the sequence of their conserved catalytic motif.
Various regions of hTTP recovered 31 proteins that fell into 12 categories based on sequence similarities.
Previously, some approaches were presented that automatically perform such transfers of functional annotations based on sequence similarities [12], [13].
Currently, 48 distinct ABC transporters have been identified in the human genome, and these can further divided into seven subfamilies (A G) based on sequence similarities [3].
In our approach we match the pyrosequencing reads to full-length, taxonomically classified, reference 16S rRNA sequences, based on sequence similarities deduced by BLAST.
Hence we targeted our search for p63-response elements (p63RE) in these potential enhancer elements based on sequence similarities to the p63 consensus site as defined by a number of laboratories, including our own [30], [31], [32], [33].
Our results provide a framework for studying molecular evolution and epidemiology of type A influenza and are a kind of new annotation to these sequences based on sequence similarities and phylogenies.
