We obtained the protein sequences encoded by DNA transposons used in these two methods from the TE-encoded protein database, available in the downloaded RepeatMasker package [ 90].
Gad-1 and Gad-2 are antimicrobial peptide (AMP) sequences encoded by paralogous genes.
The protein sequences encoded by genes 1 and 3 are identical (UniProt Knowledgebase AC P10983) [35].
Sequences encoded by different exons are shown in different colors, the sequence corresponding to the EUL domain (pFam) is underlined.
Typically, the RT domain protein sequences encoded by different non-LTR retrotransposons are similar to each other in terms of significant BLASTP E-values.
Each clone was selected using a phage display library of Z variants, and the amino acid sequences encoded by each clone are different.
For Ka/Ks estimation across shared scaffolds, all protein encoding (cDNA) sequences encoded by scaffolds from the 24 metagenomes, as well as their transcribed amino acid sequences, were downloaded from JGI's IMG/m server.
Alignments of the amino acid sequences encoded by psaA, psaB, psbA, psbC, psbD, and rbcL were constructed for phylogenetic analyses.
Likewise, for the sequences encoded by the other four biochemical properties, each is also corresponding to 21 components.
The MelC2 and MelD2 sequences encoded by these operons were also distinctly separated in phylogenetic analysis (Supporting Information, Fig. S2).
Therefore, the peptide (amino acids) sequences encoded by the DNA-dependent-DNA-polymerase (DdDp) gene of each taxon were aligned with ClustalW [33].
