BL2SEQ
We used BL2SEQ to cluster remaining protein sequences into different groups. If a local alignment of two proteins had an E-value below 10−4 and was at least 20 amino acid long, as well as the predicted Sec residues were located at the same position or very close (no more than three residues apart) in the alignment, the two proteins were assigned to the same cluster.
BL2SEQ
We used BL2SEQ to cluster remaining protein sequences into different groups. If a local alignment of two proteins had an E-value below 10−4 and was at least 20 amino acid long, as well as the predicted Sec residues were located at the same position or very close (no more than three residues apart) in the alignment, the two proteins were assigned to the same cluster.
analyzed
We analyzed the conservation of TGA-flanking regions in all six reading frames using BLASTX. If the best hit, which covered the TGA codon with at least a 10-nt overlap, was in a different reading frame than the TGA codon, the corresponding sequence was filtered out. RPS-BLAST was then used to search against conserved domains database (CDD). If the best hit which covered the TGA codon with at least a five-residue overlap was in a different reading frame or additional stop codons appeared withi...
analyzed
We analyzed the conservation of TGA-flanking regions in all six reading frames using BLASTX. If the best hit, which covered the TGA codon with at least a 10-nt overlap, was in a different reading frame than the TGA codon, the corresponding sequence was filtered out. RPS-BLAST was then used to search against conserved domains database (CDD). If the best hit which covered the TGA codon with at least a five-residue overlap was in a different reading frame or additional stop codons appeared withi...
Cys-containing
Each Cys-containing protein sequence in the NR database was initially searched against the Olavius symbionts’ metagenomic database for possible TGA/TAG/TAA-containing homologs using TBLASTN with default parameters. Only local alignments, in which Cys in the query protein was aligned with TGA codon in the nucleotide sequence from the Olavius symbionts’ metagenomic database, were selected for further analysis. For each TGA-containing nucleotide sequence identified in the metagenomic database, r...
Cys-containing
Each Cys-containing protein sequence in the NR database was initially searched against the Olavius symbionts’ metagenomic database for possible TGA/TAG/TAA-containing homologs using TBLASTN with default parameters. Only local alignments, in which Cys in the query protein was aligned with TGA codon in the nucleotide sequence from the Olavius symbionts’ metagenomic database, were selected for further analysis. For each TGA-containing nucleotide sequence identified in the metagenomic database, r...
