Table 1.
SNPs above the prevalence filter (>15%/<85%).
| UniProt BLAST annotation | General information | PROVEAN | GO term | ||||
|---|---|---|---|---|---|---|---|
| Protein name | UniProt acc. no. | Prevalence | Variant | Prediction | no. | Aspect | Info |
| Phospho-N-acetylmuramoyl-pentapeptide- transferase | A0A220PD53 | 19.0% | V340G | Deleterious | – | – | – |
| Undecaprenyldiphospho- muramoylpentapeptide beta-N-acetylglucosaminyltransferase | A0A220PD36 | 20.7% | T148A | Neutral | – | – | – |
| Dienelactone hydrolase family protein | A0A1Y0GE31 | 19.0% | – | – | GO:0016787 | F | hydrolase activity |
| Type VI secretion system Vgr family protein | A0A1G5LY91 | 19.0% | Q591L | Deleterious | – | – | – |
| Uncharacterized protein | A0A1C7C392 | 20.7% | – | – | – | – | – |
| Putative allantoin permease | A0A0P1D6C1 | 15.5% | F393L | Neutral | GO:0005215 | F | Transporter activity |
| GO:0055085 | P | Transmembrane transport | |||||
| Putative aldose 1-epimerase | A0A220PGB1 | 15.5% | Q268H | Deleterious | – | – | – |
| ATP synthase epsilon chain | Q9HT21 | 15.5% | G67A | Deleterious | GO:0046933 | F | Proton-transporting ATP synthase activity, rotational mechanism |
| GO:0015986 | P | ATP synthesis coupled proton transport | |||||
| Uncharacterized protein | A0A1G5M0Q6 | 15.5% | T106P | Neutral | – | – | – |
| Integrase | A0A220P6P1 | 20.7% | K219N | Neutral | – | – | – |
| Acyl-[acyl-carrier-protein]–UDP-N- acetylglucosamine O-acyltransferase | Q9X6P4 | 15.5% | Q100E | Deleterious | GO:0008780 | F | Acyl-[acyl-carrier-protein]-UDP-N-acetyl- glucosamine O-acyltransferase activity |
| GO:0009245 | P | Lipid A biosynthetic process | |||||
| GO:0009103 | P | Lipopolysaccharide biosynthetic process | |||||
| Putative transcriptional regulator | A0A220PB10 | 17.2% | L269S | Neutral | – | – | – |
| Phosphotransferase family protein | A0A220PAS8 | 20.7% | Q221* | Neutral | – | – | – |
| Type VI secretion system Vgr family protein | A0A1G5KZC8 | 19.0% | M411R | Deleterious | – | – | – |
| Uncharacterized protein | A0A1D5BW36 | 20.7% | N165D | Neutral | GO:0000155 | F | Phosphorelay sensor kinase activity |
| MexZ | Q9ZH26 | 19.0% | L123* | Deleterious | GO:0003677 | F | DNA binding |
| GO:0006355 | P | Regulation of transcription, DNA-templated | |||||
| GO:0006351 | P | Transcription, DNA-templated | |||||
| MerR family transcriptional regulator | A0A1S1BX29 | 15.5% | A115T | Deleterious | GO:0003677 | F | DNA binding |
| GO:0006355 | P | Regulation of transcription, DNA-templated | |||||
| Uncharacterized protein | A0A220PHL6 | 17.2% | – | – | – | – | – |
| Uncharacterized protein | A0A220PHL6 | 17.2% | – | – | – | – | – |
Cluster 2: 19 SNPs.
Only SNPs above the prevalence filter (prevalence in at least 15% of strains) and with resulting change in coded amino acid are reported, i.e., SNPs not resulting in amino acid change (non-coding SNPs) are omitted from this table. Variant annotation was performed by SnpEff. Protein function prediction was performed by PROVEAN protein with a default cutoff of −2.5. If variant is not coding, information about “variant” (general information) and “prediction” (PROVEAN) is not indicated in the table.
UniProt BLAST annotation: the best hit (by identity) is given in the table.
Bold print: Proteins discussed in the manuscript text.
(asterisk) = translation termination (stop) codon.
UniProt acc. no., UniProt accession number; no., number.