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.