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. 2013 Aug;81(8):2812–2818. doi: 10.1128/IAI.00224-13

Table 3.

Indels and SNPs in M5-90 coding sequencesa

COG category M28 M5-90 M5-90 vs M28 M5-90 vs 23457 M5-90 vs 16 M Function encoded
Not in COG A0177 A0176 IS/PS▽△ IS/PS▽△ IS/PS▽△ Sodium:dicarboxylate symporter, DUF540
A0932 A0929 FS▽ NO▽ NO▽ Transposase
A0938 A0932 NTΔ ISΔ ISΔ Conserved hypothetical protein
A1528 NO HIT FS▽ FS▽ FS▽ Conserved hypothetical protein
B0001 B0001 FSΔ FSΔ NO Replication initiation protein RepC
B0564 NO HIT FSΔ FSΔ FSΔ Conserved hypothetical protein
B0885 NO HIT FSΔ NOΔ NOΔ Hypothetical protein
B0980 NO HIT FS▽ FS▽ FS▽ Hypothetical protein
C A1137 A1129 NT▽ NT▽ NT▽ Dehydrogenase, E1 component
B0107 B0107/8 IS▽ IS▽ NO▽ O-antigen polymerase
B0947 B0946 FS▽ NO▽ NO▽ Alanine dehydrogenase
E A1463 A1458 NO1⊙ NO1⊙ NO1⊙ 5,10-Methylenetetrahydrofolate reductase
A0904 A0898 FS▽ FS▽ FS▽ tRNA (uracil-5-)-methyltransferase Gid
A2028 A2027 NT▽ NT▽ NT▽ Alcohol dehydrogenase (acceptor)
B0699 B0697 FSΔ NO NO Putative cytosolic protein
H A0776 A0775 YS1⊙ YS1⊙ YS1⊙ Riboflavin biosynthesis protein Ribd
I A1164 A1156 FS/IS▽Δ NO FS/PS▽Δ Phosphatidate cytidylyltransferase
J A1103 A1095 YS10⊙ YS10⊙ YS10⊙ Queuine tRNA-ribosyltransferase
A1261 A1255/7 FS▽Δ50⊙ FS▽Δ50⊙ FS▽Δ50⊙ Elongation factor Tu
L A0145 NO HIT FS/PSΔ FS/PSΔ FS/PSΔ Transposase
A0989 NO HIT FS▽ FS▽ FS▽ IS6501 transposase
A1215 A1208 NTΔ NO NO Recombination factor protein RarA
B0522 B0521/2 IS▽ NO▽ NO▽ Conserved hypothetical protein
M A0655 A0654/5 ISΔ ISΔ ISΔ Lytic transglycosylase catalytic
B0388 B0386 NOΔ NOΔ NOΔ LPS biosynthesis protein
B0404 B0402/3 IS▽Δ IS▽Δ IS▽Δ Conserved hypothetical protein
O A0277 A0274 NT▽ NT▽ NT▽ Conserved hypothetical protein
P A0508 A0505 NO1⊙ NO1⊙ NO1⊙ Chloride channel core protein
R A0422 A0419 NT▽ NT▽ NT▽ Methyltransferase
B0697 B0695 FSΔ FSΔ FSΔ Pyridine nucleotide-disulfide oxidoreductase
B0963 B0962 NO▽ NO▽ NO▽ WD-repeat family protein
S A0683 A0683 FS/PS▽ FS/PS▽ FS/PS▽ Conserved hypothetical protein
A0936 A0930 ISΔ ISΔ ISΔ Conserved hypothetical protein
A1618 NO HIT FSΔ FSΔ FSΔ Transcriptional regulator, Cro/cI family
U B0076 B0076 NOΔ NOΔ NOΔ Nodulation protein Nfed, C terminus only
a

Abbreviations and symbols: ⊙, single nucleotide substitution; ▽, deletion; Δ, insertion; FS, frameshift; IS, internal stop; NO, no difference; NT, N-terminal truncation; PS, premature stop; vs, versus; YS, SNP resulting in a change in the amino acid net charge; COG, clusters of orthologous groups (see Table 4). Boldface indicates ORFs with consistent differences between the complete genome sequences of the attenuated M5-90 strain versus the virulent strains.