Table 5. Nucleotide polymorphisms unique to the CDC Philadelphia strains relative to the NCBI Philadelphia-1 reference sequence.
| Strain | Nucleotide Polymorphism | No. of Polymorphisms (nt) | Nucleotide position | Nucleotide position in NCBI Philadelphia-1 | Associated ORF's | Potential Translational Importance |
|---|---|---|---|---|---|---|
| CDC Philadelphia-1 | C → A | 1 | 490,668 | 490,668 | icmG(lpg0452) | Premature stop at codon 28 |
| C → T | 1 | 894,870 | 884,511 | Upstream of Na/H antiporter (lpg0806) | Unknown | |
| Deletion | 582 | 2,143,988 | 2,133,629 | Sensory box histidine kinase (lpg1912) | In-frame deletion | |
| Ins T | 1 | 3,047,909 | 3,038,132 | Upstream of icmW (lpg2688) | Unknown | |
| Del T | 1 | 3,259,077 | 3,249,300 | ptsP (lpg2871) | Premature stop at codon 340 | |
| Philadelphia-2 | Insertion | 37,890 | 173,321 | 173,321 | Downstream of ssrA (tmRNA) | Chromosomal integration of pP36-Ph, shared with Philadelphia-4 and ATCC Philadelphia-1 |
| G → T | 1 | 418,480 | 380,590 | fusA(lpg0326) | G299C | |
| T → C | 1 | 944,447 | 896,198 | clpA(lpg0818) | F95S | |
| T → A | 1 | 1,081,176 | 1,032,927 | tldD (lpg0951) | L87M | |
| T → C | 1 | 1,504,897 | 1,456,648 | cyaA(lpg1322) | Y485C | |
| C →T | 1 | 1,562,303 | 1,514,054 | Hypothetical protein (lpg1368) | Synonymous | |
| G → A | 1 | 2,134,556 | 2,086,297 | tRNA-Leu (lpg1863) | Unknown | |
| Del T | 1 | 3,297,382 | 3,249,082 | ptsP (lpg2871) | Framshift creates premature stop at codon 375 | |
| Philadelphia-3 | Ins T | 1 | 12,618 | 12,618 | hypothetical protein (lpg0008) | Framshift creates premature stop at codon 98 |
| G → A | 1 | 142,453 | 142,452 | Cytochrom C4 (lpg0124) | Premature stop at codon 116 | |
| Del G | 1 | 609,681 | 609,680 | 16S rRNA (lpg0569) | Unknown | |
| Del G | 1 | 611,552 | 611,552 | 23S rRNA (lpg0571) | Unknown | |
| C → T | 1 | 705,342 | 695,141 | Hypothetical protein (lpg0647) | L441F | |
| T → C | 1 | 746,429 | 736,228 | Hypothetical protein (lpg0684) | F441L | |
| Del T | 1 | 1,030,855 | 1,020,497 | Hypothetical protein (lpg0941) | Premature stop at codon 749 | |
| G → A | 1 | 1,127,583 | 1,117,226 | Chemiosmotic efflux system B protein A (lpg1020) | A876T | |
| Ins T | 1 | 1,433,538 | 1,423,181 | Hydroxyacylglutathione hydrolase GloB (lpg1295) | Frameshift changes protein sequence and adds 2 amino acids | |
| Del T | 1 | 2,144,052 | 2,133,685 | Sensory box histidine kinase (lpg1912) | Framshift causes premature stop at codon 38 | |
| Del T | 1 | 3,088,004 | 3,077,599 | Hypothetical protein (lpg2725) | Frameshift creates premature stop at codon 204 | |
| G → T | 1 | 3,151,187 | 3,140,784 | nuoB2 (lpg2788) | Synonymous | |
| Deletion | 181 | 3,258,530 | 3,248,127 | ptsP (lpg2871) | Frameshift creates premature stop at codon 631 | |
| Philadelphia-4 | G → A | 1 | 7,181 | 7,181 | Intergenic region between lpg004-lpg005 | Unknown |
| Insertion | 37,890 | 173,321 | 173,321 | Downstream of ssrA (tmRNA) | Chromosomal integration of pP36-Ph, shared with Philadelphia-2 and ATCC Philadelphia-1 | |
| G → T | 1 | 40,4828 | 36,6938 | secE (lpg0316) | L55F | |
| G → A | 1 | 420,902 | 383,012 | rpsJ/nusE (lpg0328) | G34S | |
| T → C | 1 | 2,163,269 | 2,115,012 | Glutathione-regulated potassium efflux system (lpg1897) | L7P | |
| C → A | 1 | 2,442,338 | 2,394,082 | Downstream of tutC response regulator (lpg2146) | Unknown | |
| A → G | 1 | 2,539,995 | 2,491,740 | Downstream of hypothetical protein (lpg2207) | Unknown | |
| Insertion | 2 | 3,125,898 | 3,077,599 | Hypothetical protein (lpg2725) | Frameshift creates premature stop at codon 194 | |
| A → G | 1 | 3,197,722 | 3,149,427 | ftsH (lpg2796) | I478T | |
| T → C | 1 | 3,296,986 | 3,248,468 | ptsP (lpg2871) | Q495R | |
| ATCC Philadelphia-1 | Insertion | 37,890 | 173,321 | 173,321 | Downstream of ssrA (tmRNA) | Chromosomal integration of pP36-Ph, shared with Philadelphia-2 and -4 |
| C → T | 1 | 742,136 | 694,044 | Hypothetical protein (lpg0647) | T75I | |
| C → A | 1 | 3,042,468 | 2,994,210 | gacA response regulator (lpg2646) | R74L |
Ph-1, CDC Philadelphia-1; Ph-2, Philadelphia-2; Ph-3, Philadelphia-3; Ph-4, Philadelphia-4; ATCC Ph-1, ATCC Philadelphia-1