Supplementary Figure 5: Significant Pfam-A matches of PtIM of EttA with PF12848 (ABC_tran_2) domain and sequence alignment of E. coli K12-MG1655 tRNA-encoding genes.
From: EttA regulates translation by binding the ribosomal E site and restricting ribosome-tRNA dynamics
(a) HMM, hidden Markov model sequence; MATCH, the match between HMM and SEQ; PP, posterior probability, or the degree of confidence in each individual aligned residue; SEQ, query sequence. Green and cyan highlights residues in PtIM of EttA that may interact with P-site tRNAfMet and with 23S rRNA, respectively (Supplementary Table 1). (b) An alignment of all the genes coding for tRNA in E. coli MG1655 was generated using the tRNAdb3 database (http://trna.bioinf.uni-leipzig.de), highlighting the specific features of the initiator tRNA which may interact with ribosome-bound EttA-EQ2. tRNA structural features that are close to EttA-EQ2 are highlighted in yellow. The CpU bulge, present in two isoforms of Initiator tRNA (Ini) and two of three isoforms of Proline tRNA (Pro), is in green. The C1::A72 mismatch, only present in the two isoforms of initiator tRNA, is in purple. The anticodons of all the tRNAs are in red.
