TABLE 3.
RDs identified by comparative OBGS analysis and comparative genome hybridization studies of the two E. coli O157:H7 lineagesa
| RD | BLAST result and gene function and/or description | Alterationb |
|---|---|---|
| RDOBGS 1 | VT2-Sa Ssb (Ea10); hypothetical protein | SNP in OBGS priming sites (OCT1C) |
| RDOBGS 2 | Hypothetical protein from CP-933C | Large deletion (at least 700 bp) in lineage II |
| RDOBGS 3 | Z1841 to Z1842 from CP-933 | ND |
| RDOBGS 4 | Hypothetical protein; holin from Shigella flexneri phage V | Large insertion and mismatches in lineage II |
| RDOBGS 5 | NinE; putative methylase; antirepressor; phage VT2-Sa | SNP in OBGS priming sites (OCT21); large deletion and mismatches in lineage II |
| RDOBGS 6 | Hypothetical protein from phage 933W | ND |
| RDOBGS 7 | Nucleotides 301374 to 301721 from CP933H | Large deletion (at least 400 bp) in lineage II |
| RDOBGS 8 | Portal protein from Shigella flexneri phage V | Large insertion (at least 400 bp) in lineage II |
| RDOBGS 9 | Hypothetical protein from CP-933C | ND |
| RDOBGS 10 | Antitermination protein; hypothetical protein from phage VT2-Sa | ND |
| RDOBGS 11 | Putative minor tail protein | ND |
| RDOBGS 12 | Putative superinfection exclusion protein; Ssb | ND |
| RDOBGS 13 | Putative integrase from phage TPW22 | ND |
| RDOBGS 14 | Putative tail-length tape measure protein from phage HK97 | ND |
| RDOBGS 15 | Putative antirepressor; putative endolysin; hypothetical protein | SNP in OBGS priming sites (OCT21) |
| RDOBGS 16 | MokW from 933W | Large deletion (at least 1 kb) in lineage II |
| RDOBGS 17 | Hypothetical protein; Shiga toxin subunit B precursor | Large deletion (at least 1 kb) in lineage II |
| RDOBGS 18 | ECS1588 PerC-like protein | Deletion in lineage II |
| RDOBGS 19 | Z5935 | 9-bp insertion in lineage II |
| RDOBGS 20 | Putative fimbrial-like protein | Insertion and mismatches in lineage II |
| RDOBGS 21 | Putative adhesin and penetration protein | SNP in OBGS priming sites (OCT23) |
| RDOBGS 22 | FolD | 8-bp duplication in lineage II |
| RDOBGS 23 | Putative phosphotransferase system enzyme I; dihydroxyacetone kinase | Large deletion (at least 1 kb) in lineage II |
| RDOBGS 24 | Hypothetical protein; proline permease II | SNP in OBGS priming sites (OCT19) |
| RDOBGS 25 | Putative ATP-binding protein of ABC transporter | Large deletion (at least 1 kb) in lineage II |
| RDOBGS 26 | d-Ribose periplasmic binding protein; ribokinase | 9-bp deletion in lineage II |
| RDOBGS 27 | Regulator of acetyl-coenzyme A synthetase; repressor of aceBA operon | 18-bp duplication in lineage II |
| RDOBGS 28 | Putative DNA replication protein from Shigella flexneri | 50 mismatches |
| RDOBGS 29 | IS629/RepE replication protein from pO159 | ND |
| RDOBGS 30 | YjgB/LeuX | Deletions and insertions in lineage II |
| RDOBGS 31 | Repeat sequences (158 bp) | ND |
| RDOBGS 32 | Repeat sequences (22 bp) | ND |
| RDOBGS 33 | Repeat sequences (100 bp) | ND |
| RDOBGS 34 | Repeat sequences (13 to 20 bp) | ND |
| RDOBGS 35 | Putative atpase | SNP in OBGS priming sites (OCT1C) |
| RDOBGS 36 | Hypothetical protein; putative kinase | SNP in OBGS priming sites (OCT10) |
| RDOBGS 37 | Putative protein from E. coli K-12 | SNPs in OBGS priming sites (OCT14) |
| RDOBGS 38 | Hypothetical protein | 10-bp insertion in lineage II |
| RDOBGS 39 | Hypothetical protein from E. coli K-12 | SNP in OBGS priming sites (OCT5C) |
| RDOBGS 40 | Hypothetical protein | SNP in OBGS priming site (OCT6C) |
| RDOBGS 41 | Hypothetical protein from E. coli K-12 | 9-bp insertion in lineage II |
| RDOBGS 42 | Hypothetical protein | Large deletion (at least 1 kb) in lineage II |
| RDOBGS 43 | Hypothetical protein | SNP in OBGS priming sites (OCT12C) |
| RDOBGS 44 | Hypothetical protein from E. coli K-12 | SNP in OBGS priming sites (OCT6C) |
| RDOBGS 45 | YhcG | 77-bp insertion in lineage II |
| RDOBGS 46 | YcbC | SNPs in OBGS priming sites (OCT10, 6C) |
| RDOBGS 47 | No hit | Large insertion (at least 500 bp) in lineage II |
| RDOBGS 48 | ECs1091, ECs2182, and ECs2737; pchABC-like | ND |
| RDOBGS 49 | No hit | Large insertion (at least 500 bp) in lineage II |
| RDOBGS 50 | No hit | Large insertion (at least 350 bp) in lineage II |
| RDOBGS 51 | No hit | Large insertion (at least 500 bp) in lineage II |
| RDOBGS 52 | No hit | Large insertion (at least 300 bp) in lineage II |
| RDOBGS 53 | No hit | Large insertion (at least 150 bp) in lineage II |
| RDCGH 1 | Z0165 (hemL) | Deletion in lineage II |
| RDCGH 2 | Z0268 to Z2069 (open reading frames in Rhs element) | Deletion in lineage II |
| RDCGH 3 | Z0318 (pinH from CP-933H); same as RDOBGS 7 | Deletion in lineage II |
| RDCGH 4 | Z196 to Z1204 (perC-like region of TAI) | Deletion in lineage II |
| RDCGH 5 | Z1961 (prrA) to Z1962 (modD) | Deletion in lineage II |
| RDCGH 6 | Z2185 (hypothetical protein) to Z22186 (hypothetical protein) | Deletion in lineage II |
| RDCGH 7 | Z2207 (hypothetical oxidoreductase) | Deletion in lineage II |
| RDCGH 8 | Z2706 to Z2707 (ynhG-ynhA) | Deletion in lineage II |
| RDCGH 9 | ECs4889 to ECs4903 (phage tail region) | Deletion in lineage II |
a
Pch-containing RDs are in bold.
b
ND, not determined.