TABLE 1.
Single-nucleotide differences in L. lactis MG1363, revised relative to the previously published genomeb
| Reference positiona | Variation type | Nucleotide change | Region and/or gene or product | Amino acid change or frameshift | ORF |
|---|---|---|---|---|---|
| 26455 | SNP | T→C | Intergenic | ||
| 218270 | DIP | —→C | Gene CDS, hypothetical protein | Change frameshift | llmg_0227 |
| 311626 | SNP | T→C | Gene CDS, lmrC | Cys→Arg | llmg_0324 |
| 549522 | DIP | —→T | Intergenic | ||
| 589181 | DIP | —→C | Intergenic | ||
| 594325 | SNP | T→A | Gene CDS, recJ | Ile→Lys | llmg_0606 |
| 617310 | SNP | A→C | Gene CDS, divalent cation transport-related protein | Synonymous | llmg_0628 |
| 672541 | SNP | A→T | Gene CDS, hypothetical protein | Synonymous | llmg_0681 |
| 672705 | SNP | T→G | Intergenic | ||
| 674847 | DIP | A→— | Intergenic | ||
| 876869 | SNP | C→G | Gene CDS, amtB | His→Asp | llmg_0910 |
| 894625 | DIP | —→G | Gene CDS, hypothetical protein | Change frameshift | llmg_0924 |
| 912618 | SNP | T→A | Gene CDS, hypothetical protein | Leu→Gln | llmg_0944 |
| 912718 | SNP | T→A | Gene CDS, hypothetical protein | Asn→Lys | llmg_0944 |
| 977526 | DIP | C→— | Gene CDS, lplA | Change frameshift | llmg_1011 |
| 1007288 | SNP | C→T | Gene CDS, bglP | Synonymous | llmg_1045 |
| 1061785 | SNP | A→T | Gene CDS, putative secreted protein | Ile→Asn | llmg_1101 |
| 1093300 | DIP | —→C | Gene CDS, cell wall surface anchor family protein | Change frameshift | llmg_1127 |
| 1093563 | DIP | —→C | Gene CDS, hypothetical protein | Change frameshift | llmg_1128 |
| 1167414 | SNP | T→G | Intergenic | ||
| 1210279 | DIP | —→A | Pseudogene | llmg_pseudo_39 | |
| 1223555 | DIP | G→— | Intergenic | ||
| 1277684 | SNP | T→A | Gene CDS, hypothetical protein | Asn→Ile | llmg_1306 |
| 1492365 | SNP | T→A | Gene CDS, kinE | Synonymous | llmg_1518 |
| 1500910 | SNP | C→A | Gene CDS, hypothetical protein | Asp→Glu | llmg_1528 |
| 1532424 | SNP | G→C | Gene CDS, stress-induced DNA-binding protein | Pro→Arg | llmg_1560 |
| 1572256 | SNP | T→A | Intergenic | ||
| 1572258 | SNP | G→A | Intergenic | ||
| 1588193 | SNP | T→G | Gene CDS, ugd | Gln→Pro | llmg_1616 |
| 1588245 | SNP | T→A | Gene CDS, ugd | Thr→Ser | llmg_1616 |
| 1588246 | SNP | A→T | Gene CDS, ugd | Asn→Lys | llmg_1616 |
| 1588356 | SNP | T→A | Gene CDS, ugd | Asn→Tyr | llmg_1616 |
| 1610761 | SNP | T→C | Gene CDS, hypothetical protein | Ile→Val | llmg_1634 |
| 1614129 | DIP | —→T | Gene CDS, mleP | Change frameshift | llmg_1637 |
| 1660050 | DIP | —→T | Intergenic | ||
| 1681037 | SNP | T→C | Gene CDS, pepV | Glu→Gly | llmg_1706 |
| 1731090 | SNP | T→C | Gene CDS, hypothetical protein | Synonymous | llmg_1749 |
| 1826407 | SNP | A→G | Gene CDS, metal-dependent hydrolase | Synonymous | llmg_1845 |
| 1826460 | DIP | —→T | Intergenic | ||
| 1838903 | SNP | T→C | Gene CDS, rmaB | Thr→Ala | llmg_1860 |
| 1853472 | SNP | C→A | Gene CDS, glgP | Met→Ile | llmg_1871 |
| 1854998 | SNP | T→A | Gene CDS, glgA | Synonymous | llmg_1872 |
| 1891450 | SNP | C→A | Gene CDS, hypothetical protein | Trp→Leu | llmg_1911 |
| 1916379 | DIP | T→— | Pseudogene | llmg_pseudo_59 | |
| 1921434 | DIP | T→— | Gene CDS, hypothetical protein | Change frameshift | llmg_1941 |
| 1921461 | DIP | C→— | Gene CDS, hypothetical protein | Change frameshift | llmg_1941 |
| 1921473 | DIP | C→— | Gene CDS, hypothetical protein | Change frameshift | llmg_1941 |
| 1921516 | SNP | C→T | Intergenic | ||
| 1921529 | DIP | T→— | Intergenic | ||
| 1921636 | DIP | T→— | Intergenic | ||
| 1921651 | DIP | T→— | Intergenic | ||
| 1921655 | DIP | G→— | Intergenic | ||
| 1921664 | DIP | T→— | Intergenic | ||
| 1921674 | DIP | A→— | Intergenic | ||
| 1921680 | DIP | T→— | Intergenic | ||
| 1921693 | DIP | G→— | Intergenic | ||
| 1921702 | DIP | A→— | Intergenic | ||
| 1921707 | DIP | T→— | Intergenic | ||
| 1921717 | DIP | T→— | Intergenic | ||
| 1921724 | DIP | A→— | Intergenic | ||
| 1921743 | DIP | T→— | Intergenic | ||
| 1921753 | DIP | A→— | Intergenic | ||
| 1921776 | DIP | T→— | Intergenic | ||
| 1921788 | DIP | G→— | Intergenic | ||
| 1933214 | SNP | G→C | Gene CDS, atpB | Synonymous | llmg_1951 |
| 1933215 | SNP | C→G | Gene CDS, atpB | Gly→Ala | llmg_1951 |
| 1935399 | DIP | T→— | Pseudogene, comEC | llmg_pseudo_60 | |
| 1942432 | SNP | T→C | Gene CDS, hypothetical protein | Ile→Val | llmg_1960 |
| 1942730 | SNP | C→A | Intergenic | ||
| 2112671 | DIP | —→T | Intergenic | ||
| 2122554 | SNP | G→A | Gene CDS, cfa | Ser→Leu | llmg_2161 |
| 2122558 | SNP | C→T | Gene CDS, cfa | Ala→Thr | llmg_2161 |
| 2230258 | DIP | A→— | Gene CDS, hypothetical protein | Change frameshift | llmg_2272 |
a
Location is based on the previously published genome sequence of L. lactis MG1363 (GenBank accession number AM406671).
b
Abbreviations: SNP, single-nucleotide polymorphism; DIP, single-nucleotide indel; CDS, coding sequence; ORF, open reading frame; —, gap.