TABLE 1.
Nucleotide and coding differences identified between genomes of Rlow and Rhigh
| Rlow |
Nucleotide difference (Rlow/Rhigh)d | Rhigh |
Locus and/or protein/region | Effect on Rhigh codingb | ||
|---|---|---|---|---|---|---|
| Position (nt)a | Lengthc | Position (nt)a | Length | |||
| 15684 | 1 | G/T | 15684 | 1 | MGA_0644, glycerol kinase | Stop; 157-aa truncation |
| 46081 | 1 | C/T | 46081 | 1 | MGA_0677, glycerol-3-phosphate transport protein | T417I substitution |
| 65904 | 1 | A/C | 65904 | 1 | MGA_0704, conserved membrane protein | Y64D substitution |
| 218873 | 54 | Repeat/— | 218872 | 0 | MGA_0928, adherence-associated protein Hlp3 | 18-aa deletion |
| 223599 | 0 | —/A | 223546 | 1 | MGA_0934, cytadhesin GapA | Frameshift out 995 aa |
| 255751 | 6 | GAA repeat | 255697 | 0 | Intergenic, VlhA4.03 promoter region | |
| 255971 | 12 | Repeat/— | 255911 | 0 | MGA_0968, VlhA4.03a N-terminal fragment | TPNP repeat deletion |
| 260507 | 3 | GAA repeat | 260435 | 0 | Intergenic, VlhA4.05 promoter region | |
| 262821 | 9 | GAA repeat | 262746 | 0 | Intergenic, VlhA4.06 promoter region | |
| 265255 | 3 | GAA repeat | 265171 | 0 | Intergenic, VlhA4.07 promoter region | |
| 269969 | 3 | GAA repeat | 269882 | 0 | Intergenic, VlhA4.07.2a promoter region | |
| 270185 | 0 | —/Repeat | 270097 | 12 | MGA_1336, VlhA4.07.2.a | TP repeat insertion |
| 272304 | 0 | GAA repeat | 272228 | 3 | Intergenic, VlhA4.07.3 promoter region | |
| 274692 | 6 | GAA repeat | 274617 | 0 | Intergenic, VlhA4.07.4 promoter region | |
| 277009 | 9 | GAA repeat | 276928 | 0 | Intergenic, VlhA4.07.5 promoter region | |
| 279442 | 0 | GAA repeat | 279354 | 15 | Intergenic, VlhA4.07.6 promoter region | |
| 282061 | 6 | Repeat/— | 281986 | 0 | MGA_0979, VlhA4.08 | TP repeat deletion |
| 284335 | 1 | T/C | 284255 | 1 | Intergenic, VlhA4.09 | |
| 284341 | 1 | G/A | 284261 | Intergenic, VlhA4.09 | ||
| 284396 | 6 | Repeat/- | 284315 | 0 | MGA_0981, VlhA4.09 | TP repeat deletion |
| 291716 | 6 | GAA repeat | 291629 | 0 | Intergenic, VlhA4.12 promoter region | |
| 307991 | 3 | ATG/— | 307898 | 0 | MGA_1000, RNA polymerase subunit beta | D repeat deletion |
| 358895 | 18 | Repeat/— | 358799 | 0 | MGA_1071, conserved hypothetical protein | TPTPTP repeat deletion |
| 389142 | 1 | C/G | 389029 | 1 | Intergenic, asparaginyl-tRNA synthetase | |
| 393735 | 0 | —/G | 393623 | 1 | MGA_1117/9, CrmB-like protein | ORF fusion |
| 421612 | 1 | G/A | 421500 | 1 | MGA_1161, conserved hypothetical protein | S323N substitution |
| 448139 | 0 | —/Repeat | 448028 | 17 | MGA_1199, fibronectin binding protein PlpA | Frameshift out 166 aa |
| 480523 | 0 | GAA repeat | 480429 | 3 | Intergenic, VlhA5.03 promoter region | |
| 483041 | 0 | GAA repeat | 482950 | 6 | Intergenic, VlhA5.04 promoter region | |
| 487897 | 9 | GAA repeat | 487810 | 0 | Intergenic, VlhA5.06 promoter region | |
| 490341 | 0 | GAA repeat | 490247 | 33 | Intergenic, VlhA5.07 promoter region | |
| 492725 | 0 | GAA repeat | 492664 | 3 | Intergenic, VlhA5.08 promoter region | |
| 495034 | 3 | GAA repeat | 494974 | 0 | Intergenic, VlhA5.09 promoter region | |
| 495312 | 13 | 13 bp/7 bp | 495250 | 7 | MGA_1251, VlhA5.09 | TP repeat deletion |
| 497434 | 48 | GAA repeat | 497365 | 0 | Intergenic, VlhA5.10 promoter region | |
| 499881 | 18 | GAA repeat | 499764 | 0 | Intergenic, VlhA5.11 promoter region | |
| 594921 | 3 | GAA repeat | 594786 | 0 | Intergenic, VlhA1.02 promoter region | |
| 597248 | 12 | GAA repeat | 597110 | 0 | Intergenic, VlhA1.03 promoter region | |
| 599667 | 6 | GAA repeat | 599517 | 0 | Intergenic, VlhA1.04 promoter region | |
| 606824 | 0 | GAA repeat | 606670 | 12 | Intergenic, VlhA1.06 promoter region | |
| 609365 | 12 | GAA repeat | 609221 | 0 | Intergenic, VlhA1.07 promoter region | |
| 611661 | 3 | GAA repeat | 611505 | 0 | Intergenic, VlhA1.08 promoter region | |
| 657054 | 1 | A/C | 656896 | 1 | MGA_0141, nucleotide phosphodiesterase | N56K substitution |
| 670334 | 6 | Repeat/— | 670175 | 0 | MGA_0162, dihydrolipoamide acetyltransferase | GG repeat deletion |
| 672071 | 0 | —/CTT | 671908 | 3 | MGA_0165, pyruvate dehydrogenase E1 subunit | E repeat insertion |
| 677821 | 0 | —/TGTATTTG (repeat) | 677661 | 8 | MGA_0173, TlyC-like protein | Frameshift out 67 aa |
| 711767 | 0 | —/GA (repeat) | 711615 | 2 | MGA_0221, ABC peptide transport permease | Frameshift out 99 aa |
| 713340 | 20 | Repeat/— | 713188 | 0 | MGA_0223/4, ABC peptide transport permease | ORF fusion |
| 723519 | 1 | T/C | 723348 | 1 | MGA_0237, ABC peptide transport solute BP | D467G substitution |
| 736772 | 0 | —/T (repeat) | 736602 | 1 | MGA_0250, unique hypothetical | 61-aa N-terminal extension |
| 740191 | 37 | Repeat/— | 740020 | 0 | MGA_0256/8, phase variable protein PvpA | ORF fusion |
| 757659 | 12 | Repeat/— | 757451 | 0 | MGA_0287, amino acid permease | 4-aa C-terminal deletion |
| 815905 | 3 | GAT/— | 815685 | 0 | MGA_0368, ABC transport permease | I repeat deletion |
| 821389 | 0 | GAA repeat | 821168 | 21 | Intergenic, VlhA3.01 promoter region | |
| 822227 | 0 | —/ATAT (repeat) | 822027 | 4 | MGA_0379, VlhA3.02 | Frameshift out 218 aa |
| 823701 | 0 | GAA repeat | 823505 | 3 | Intergenic, VlhA3.02 promoter region | |
| 828562 | 12 | GAA repeat | 828367 | 0 | Intergenic, VlhA3.05 promoter region | |
| 833126 | 0 | —/TGGAGT | 832921 | 6 | MGA_0388, VlhA3.06 | TP repeat insertion |
| 835662 | 0 | GAA repeat | 835463 | 12 | Intergenic, VlhA3.07 promoter region | |
| 840488 | 3 | GAA repeat | 840299 | 0 | Intergenic, VlhA3.09 promoter region | |
| 910723 | 581 | 581 bp/— | 910531 | 0 | MGA_0508, fructose-specific PTS component | N-terminal deletion |
| 929813 | 66 | Repeat/— | 929040 | 0 | CRISPR | Repeat deletion |
| 930766 | 0 | —/Repeat | 929929 | 66 | CRISPR | Repeat insertion |
| 938625 | 1 | A/— (repeat) | 937852 | 0 | Intergenic, MGA_0536 ATPase and MGA_0537 hsdM | |
a
nt, nucleotide.
b
aa, amino acids.
c
Length in nucleotides.
d
Specific nucleotides, length of nucleotide sequences, and/or the presence of repeated sequences noted as indels or substitutions between Rlow and Rhigh are given.