Identification and characterization of PIM gene family in tree
sparrow and zebra finch
The PIM protein sequences of human (PIM1, PIM2 and PIM3) and chicken
(PIM1 and PIM3) were obtained from UniProt database and then used as
query to search against the tree sparrow and zebra finch (downloaded
from NCBI database) protein dataset using the BLASTP program in BLAST+
(Camacho et al., 2009) with and e-value of 1e-5 and identity of 50% as
the threshold. We used the Hidden Markov Model (HMM) of protein kinase
domain (PF00069) to reconfirm the predicted PIM protein sequences using
HMMER v3.3.2 (Eddy, 2011). Furthermore, the putative PIM sequences with
incomplete protein kinase domain which related with the protein kinase
catalytic activity were discarded by searching manually using online
HmmerWeb v2.41.2 (Potter et al., 2018). Ultimately, there are 6 PIM
sequences left for zebra finch and 143 for tree sparrow. The molecular
weight (MW) and isoelectric points (PI) of PIM proteins of tree sparrow
were calculated by Peptides v2.4.4 (Osorio et al., 2015). We used
FastTree v2.1.10 (Price et al., 2010) to construct a ML tree and MEME
v5.4.1 (Bailey et al., 2015) to analyze the conserved motif structures
of a total of 154 full-length amino acid sequences of PIM family (2 of
chicken, 3 of human, 6 of zebra finch and 143 of tree sparrow). The
combination of constructed ML tree and predicted motif structure of PIM
family were visualized by iTOL.