TABLE 2.

Significant sequence divergences of pC15-1a from R100

VariationaR100 coordinatesbEffect in pC15-1ac
Substitution29694G-to-T substitution introduces stop codon and truncates ycjB
Deletion29885-29902After the early stop introduced by substitution above in pC15-1a, a 6-aa deletion (LLLLLL) in the R100 ycjB region
Deletion30210C deleted; causes frameshift in ydaA approximately midway in ORF; resulting protein diverges at this point
Deletion33242-332472-aa deletion (SS; AGTAGC) in repetitive region of yddA
Deletion36157-45253Deletion of Tn10; inverted repeats from IS10-L and IS10-R are still present
Insertion47797/47798IS682 variant (not 100% identical); disrupts yehA; last 8 aa originate from IS682 sequence
Insertion48227/482281-bp insertion in noncoding region downstream of yehA
Deletion58087-58489AAC deleted; causes fusion of yfhA and yfiA; last 28 aa of ORF are from yfiA
Substitution65886T-to-G substitution eliminates stop between traN and traZ; also noted in R100-1 (AF005044)
Deletion78171-781876-aa deletion (PQQPQQ; CCACAACAGCCACAACAG) in repetitive region of traD
Insertion86627-866281-bp insertion in noncoding region downstream of yigA
Insertion86648-86649IS1a inserted here; found in R100 but located in region not contained in pC15-1a
Insertion86640-866488-bp insertion site of IS1a (GGTGCTATT); duplicated in pC15-1a as direct repeats flanking IS1a
  • a Nucleotide substitutions were included only if they affected the length or arrangement of the R100 coding regions. Locations of deletions in repetitive regions are arbitrary.

  • b Based on GenBank accession number AP000342.

  • c Effect of the change at the R100 coordinates on the equivalent region in the pC15-1a R100-derived region. aa, amino acids; ORF, open reading frame.