analyses provided evidence supporting the similarity of these sequences to other molluscan clock-related proteins and a closer affinity to mammalian orthologs than those of Drosophila (Supplementary Tables 2, 3, available online).
We performed predicted gene functional classification by querying protein sequences of the genes against the Kyoto encyclopedia of genes and genomes (KEGG) database using BLASTP
with Evalues <1 x [10.sup.-5].
with default parameters was used to remove duplicate proteins within plasmid sequences using a similarity score defined by the formula (length of matching sequence)*(BLAST identity score)/(length of reference protein + length of matching sequence) >0.45--that is, proteins with scores >0.45 were considered to be duplicates .
revealed that the deduced amino acid sequence of Bdor[alpha]6 was highly conserved with alpha6 homolog in other insect species.
El analisis de BLASTP
comprobo que la proteina PhaC1 y PhaC2 de la cepa Pseudomonas fluorecens IBUN S1602 presentan un alto grado de similaridad con las reportadas en las bases de datos para sintasa.
As comparacoes entre sequencias foram realizadas utilizando-se os programas BLASTn e BLASTp
do NCBI (http://www.ncbi.nlm.nih.gov).
tuberculosis and HIV, by a detailed basic local alignment search tool for proteins (BLASTP
) of the leprosy and tuberculosis genes and HIV, might give an insight into the common regions of the three which, in turn, would be helpful in developing a diagnostic tool or a vaccine for one and/or all of these highly infectious diseases.
Molecular characterization of this new point mutation is ongoing; although two tyrosine kinase proteins (ABL and IRK) naturally present this amino acid substitution, the amino acid sequence N[H.sub.2]-NLLGACT-COOH in which we found the mutation, and it is extremely conserved with respect to other known tyrosine kinase receptors, such as vascular endothelial growth factor receptor, c-KIT, and platelet-derived growth factor receptor (BLASTP
analysis; data not shown).
Orthologous groups of genes from plasmids or chromosomes were identified using BLASTp
and Inparanoid .
hits were typically around 500 AA and mapped primarily to the conserved six-transmembrane ion pore domain or to the N-terminal part of the TRP query proteins.
Gene annotation was performed using TransDecoder, implemented within Trinity, and we applied several developer-recommended gene annotation tools such as blastx and blastp
. Finally, using Trinotate, we extracted information on annotated genes applying the default options.