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Figure 3 | BMC Genomics

Figure 3

From: Conservation analysis of the CydX protein yields insights into small protein identification and evolution

Figure 3

Confirmation of functionality of CydX homologues. (A) Alignment of protein sequences of CydX homologues from Escherichia coli and other bacteria species. The small protein from Burkholderia sp. 383 (“Burkholderia383”) is not thought to be a homologue and was included as a negative control for the assay. Based on its significant sequence divergence was included in a separate alignment. (B) Alignment of the E. coli CydX protein with the CydZ protein from Klebsiella pneumoniae. (C) Assay of complementation of the ΔcydX β-mercaptoethanol sensitivity phenotype by expression of potential CydX homologues, a false positive from the tblastn search (Burkholderia sp. 383), and an unrelated small protein (CydZ) from a different bacterial species. Sensitivity was measured using zones of inhibition, and the diameter of the zone after addition of 10 μL of 12 M β-mercaptoethanol to a plate of bacteria is shown. Species are as follows: Escherichia coli (“Escherichia”), Pectobacterium atrosepticus (“Pectobacterium”), Burkholderia xenovorans (“Burkholderia”), Actinobacillus pleuropneumoniae (“Actinobacillus”), Burkholderia sp. 383 (“Burkholderia sp. 383”), Klebsiella pneumoniae (“Klebsiella”), Cellvibrio japonicus Ueda107 (“Cellvibrio”), Methylibium petroleiphilum PM1 (“Methylibium”), Haemophilus influenzae 10810 (“Haemophilus”), and Francisella philomiragia subsp. Philomiragia ATCC 25017 (“Francisella”). Alignments were generated using the program MUSCLE [57]. Amino acids are colored based on their properties at physiological conditions as follows: red amino acids are hydrophobic, green residues are hydrophilic, purple residues are positively-charged and blue residues are negatively-charged. ‘*’ indicates that the residues are identical in all sequences and ‘:’ and ‘.’, respectively, indicated conserved and semi-conserved substitutions as defined by MUSCLE.

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