TABLE 2.
Genomic DNA variants in the ET straina
| Protein | Length (amino acids) | Amino acid variant | Confidence (Q) value | Annotation |
|---|---|---|---|---|
| Energy and metabolism | ||||
| Cphy3925 (AdhE) | 872 | G609D | 8,929 | Fe-dependent bifunctional acetaldehyde-CoA/alcohol dehydrogenase |
| Cphy0215 (RnfA) | 191 | C26S | 5,569 | Ferredoxin:NAD+ oxidoreductase (Fno); couples electron transfer from reduced ferredoxin to NAD+ with cation transport out of the cell to create an electrochemical gradient |
| Cphy3255 | 259 | 20-bp insertion at Q91 | 15,938 | FMN-dependent nitroreductase |
| Transport | ||||
| Cphy0543 (MgtA/MgtB) | 920 | K417N | 8,661 | P-type ATPase for Mg2+ uptake transporter or Ca2+/Mg2+ antiporter |
| Cphy3778 | 258 | 1-bp deletion, Y239 frameshift | 11,687 | Na+ efflux transporter, ABC-2 transmembrane permease (PFAM accession no. PF06182) |
| Membrane and cell wall | ||||
| Cphy0233 (PlsD) | 237 | D80N | 9,246 | Membrane synthesis: glycerol-3-phosphate acyltransferase; transfers a fatty acid to the 1 position of glycerol-3-phosphate |
| Cphy0107 (MurC) | 469 | G115D | 8,841 | Peptidoglycan synthesis: ATP-dependent ligation of l-alanine and UDP-N-acetylmuramic acid to form UDP-N-acetylmuramyl-l-alanine |
| Gene regulation | ||||
| Cphy3040 | 301 | D182N | 8,214 | LysR transcriptional activator/repressor |
| Cphy3687 (PolB) | 1,278 | D189Y | 8,824 | β-Subunit of DNA-directed RNA polymerase |
| Noncoding changes | ||||
| Cphy0267 | 524 | Q65Q (synonymous) | 7,470 | Modification methyltransferase |
| Intergenic G→T transversion | None | 52 | Transversion between 2 convergently transcribed genes, encoding Cphy1313 and Cphy1314 | |
| Cphy3036 (ApbE) | 381 | L244L (synonymous) | 9,011 | Thiamine biosynthesis: membrane-associated lipoprotein |
a
Data include the gene name, encoded protein length, amino acid (if coding) or DNA variant, confidence value (Q) of the variant call, and annotation of the mutated protein. The probability (P) that a variant exists in the genome is reported as a Phred-scaled probability, i.e., Q = −10 × log10(1 − P), meaning that a Q value of 100 indicates an error probability (1 − P) of 10−10 (see GATK reports in the supplemental material for more information). FMN, flavin mononucleotide.