Spreadsheet: 5d284325-a4c8-4dec-92c8-dd9ec56e09b1
Sheet: Sheet1

Table S1. Regions of difference (RODS) in the EAEC 042 genome | Unnamed: 1 | Unnamed: 2 | Unnamed: 3 | Unnamed: 4
ROD ID | Start | end | size (bp) | notes
ROD1 | 21439 | 25167 | 3728 | Fimbrial operon 1. Present in 0157:[NAME], absent in UPEC CFT073
[NAME] | 156371 | 162896 | 6525 | Fimbrial operon 2. Sequence divergence between 0157:[NAME] and UPEC CFT073 strains.
ROD3 | 243529 | 276096 | 32567 | Genomic island.Sequence divergence between 0157:[NAME] and UPEC CFT073 strains. Contains Type 6 secretion system, putative macrophage toxin, phage-like protein, group II intron
ROD4 | 284682 | 323159 | 38477 | Flag-2 locus. Unique to 042
ROD5 | 336238 | 351866 | 15628 | Sequence divergence between 0157:H7 Sakai:H7 Sakai and UPEC CFT073 strains, 0157:H7 Sakai:H7 Sakai contains cryptic prophage cryptic prophage CP-933, next to tRNA
ROD6 | 390402 | 394451 | 4049 | Present in 0157:H7 Sakai:H7 Sakai, absent in UPEC CFT073, Haemagluttinin repeat autotransporter protein
ROD7 | 420665 | 424021 | 3356 | Present in 0157:H7 Sakai:H7 Sakai, absent in UPEC CFT073, cyn operon (regulator, carbonic anhydrase, cyanase, cyanate transport)
ROD8 | 430447 | 439230 | 8783 | Present in 0157:[NAME], absent in UPEC CFT073, 3-hydroxyphenylpropionate degradation operons
ROD9 | 579409 | 608257 | 28848 | Present in 0157:[NAME], absent in UPEC CFT073, RTX-family protein (pseudogene?), transporter proteins (ABC, efflux, HlyD), YadA domain protein
ROD10 | 646229 | 652504 | 6275 | Fimbrial operon 4. Present in 0157:[NAME], absent in UPEC CFT073.
ROD11 | 660240 | 671196 | 10956 | Absent in UPEC CFT073, divergent in 0157:[NAME], hypothetical proteins and transposase. 0157:[NAME] has RHS-type protein in equivalent region
ROD12 | 751327 | 758991 | 7664 | Present in 0157:[NAME], absent in UPEC CFT073, hypothetical protein and Hsp70-like protein
[NAME] | 809925 | 814805 | 4880 | Fimbrial operon 5. Absent in UPEC CFT073, divergent in 0157:[NAME]
[NAME] | 827773 | 840750 | 12977 | Present in 0157:[NAME], absent in UPEC CFT073, [NAME]. metabolism (fermentation of glutamate?) (regulator, cob(I)yrinic acid a,c-diamide adenosyltransferase, fumarate hydratase, methylaspartate ammonia-lyase, methylaspartate mutase E chain, glutamate mutase, methylaspartate mutase S chain)
ROD15 | 877116 | 917926 | 40810 | prophage 1. Absent in UPEC CFT073, divergent in 0157:[NAME] (in 0157:H7 Sakai O-island #36; cryptic prophage CP-933K), prophage, carrying bactoprenol glucosyl transferase, involved in O antigen modification, like Salmonella bacteriophage P22
ROD16 | 932121 | 934045 | 1924 | Unique to 042, 4 hypothetical protein, part of an operon, upstream CDs is pseudogene
ROD17 | 1338337 | 1341800 | 3463 | Partially present in 0157:[NAME], absent in UPEC CFT073, regulator and putative adhesion and penetration protein, in O157 putative adhesion and penetration protein is present as a fragment and regulator is missing
ROD18 | 1396781 | 1450149 | 53368 | prophage 2. Absent in UPEC CFT073, divergent prophage in 0157:[NAME], prophage, edge of rearrangement in 0157:[NAME] (EDL, not Sakai), other edge see ROD26
[NAME] | 1493439 | 1502327 | 8888 | Present in 0157:[NAME], absent in UPEC CFT073, misc amino metabolism (transporter, glutamine synthetase, 4-aminobutyrate aminotransferase)
ROD20 | 1521942 | 1527324 | 5382 | Present in 0157:[NAME], absent in UPEC CFT073, aminobenzoyl-glutamate utilization proteins (regulator, transporter, 2 utilization proteins)
ROD21 | 1533876 | 1584276 | 50400 | prophage 3. Absent in UPEC CFT073, divergent in 0157:[NAME], prophage, carrying iron transport proteins (x4)
ROD22 | 1655792 | 1659600 | 3808 | Sequence divergence between 0157:[NAME] and UPEC CFT073 strains, hypothetical proteins
ROD23 | 1671084 | 1674933 | 3849 | Present in 0157:[NAME], absent in UPEC CFT073, hypothetical proteins ([NAME]) and porin
ROD24 | 1686155 | 1692119 | 5964 | Present in 0157:[NAME], absent in UPEC CFT073, ABC transport system and D-Ala-D-Ala dipeptidase, Zn-dependent
ROD25 | 1724477 | 1738611 | 14134 | Present in 0157:[NAME], absent in UPEC CFT073, misc region ([NAME] domain protein (pseudogene?), carbohydrate kinase, regulators, ABC transporter, aldolase)
ROD26 | 1763886 | 1811200 | 47314 | prophage 4. Absent in UPEC CFT073, divergent in 0157:[NAME], carrying exonuclease, edge of rearrangement in 0157:[NAME] (EDL, not Sakai), other edge see ROD18
ROD27 | 1832521 | 1843545 | 11024 | prophage like region. Unique to 042
ROD28 | 2052698 | 2058847 | 6149 | Present in 0157:[NAME], absent in UPEC CFT073, misc utilization operon (regulator, tartrate dehydrogenase/decarboxylase, putative betaine/choline/glycine transport protein and [NAME]. dioxygenase)
ROD30 | 2214943 | 2256641 | 41698 | Prophage 5. Absent in UPEC CFT073, divergent in 0157:[NAME], carrying exonuclease VIII
ROD30A | 2256892 | 2272385 | 15493 | prophage 6. Absent in UPEC CFT073, divergent in 0157:[NAME], carrying exonuclease VIII
ROD31 | 2273544 | 2305391 | 31847 | Present in UPEC CFT073, absent in 0157:[NAME], putative siderophore cluster (regulation, biosysnthesis, transport and receptor)
ROD32 | 2321564 | 2346166 | 24602 | Genomic island 1. Absent in 0157:[NAME], divergent in UPEC CFT073, carries transposases, hypothetical proteins and [NAME] domain-containing autotransporter protein)
ROD33 | 2363198 | 2399367 | 36169 | Sequence divergence between 0157:[NAME] and UPEC CFT073 strains, O antigen genes (x5) O-antigen gene cluster
ROD34 | 2551911 | 2560079 | 8168 | prophage-like. Unique to 042, [NAME]. island, regulator similar to transcriptional activator of eaeA/bfpA expression in enteropathogenic E.coli, proQ, structural element that influences the osmotic activation of proP at a posttranslational level), possible prophage fragment, inserted next to tRNA, no repeat flanking island
ROD35 | 2591914 | 2599164 | 7250 | Present in UPEC CFT073, absent in 0157:[NAME], fatty acid utilization operon (regulators, transporter and transferases)
[NAME] | 2621345 | 2624617 | 3272 | Present in 0157:[NAME], absent in UPEC CFT073, [NAME]. islet (Major Facilitator Superfamily protein-pseudogene, regulator and hypothetical protein)
ROD37 | 2721628 | 2728077 | 6449 | Fimbrial operon 8. Sequence divergence between 0157:[NAME] and UPEC CFT073 strains
ROD38 | 2739033 | 2746934 | 7901 | Present in UPEC CFT073, divergent in 0157:[NAME], putative autotransporter protein-pseudogene (lacking N-terminal region) and transposases, probable deletion in 042
ROD39 | 2844204 | 2857834 | 13630 | Present in 0157:[NAME], absent in UPEC CFT073, anaerobic respiration operon (Hydrogenase 4 and Formate hydrogenlyase, regulator)
ROD40 | 2878688 | 2890486 | 11798 | Present in UPEC CFT073, absent in 0157:[NAME]. carries three outer membrane proteins similar to proteins on CS54 island of Salmonella enterica serotype typhimurium
ROD41 | 2922497 | 2927740 | 5243 | Present in 0157:[NAME], absent in UPEC CFT073, 3-phenylpropionic acid catabolism operon
ROD42 | 3011744 | 3038096 | 26352 | plasmid-like island, inserted next to tmRNA, no flanking repeats, sequence divergence between 0157:[NAME] and UPEC CFT073 strains. Carries plasmid replication proteins, H-NS histone family proteins. Similar to a region in Erwinia atroseptica genome,
ROD43 | 3100520 | 3104680 | 4160 | Present in 0157:[NAME], absent in UPEC CFT073, ascBF operon (regulator, PTS protein and 6-phospho-beta-glucosidase
ROD44 | 3124076 | 3126897 | 2821 | Present in 0157:[NAME], divergent in UPEC CFT073. Three subunits of hydroxyarylic acid decarboxylases/phenol carboxylase and their regulator
ROD45 | 3138650 | 3147169 | 8519 | CRISPR-associated genes. Present in 0157:[NAME], absent in UPEC CFT073, repeat array region is a different size to those found in 0157:[NAME]
ROD46 | 3249573 | 3276731 | 27158 | Type III secretion system. Present in 0157:[NAME], absent in UPEC CFT073, part of this region is in [NAME] (not TTSS)
ROD47 | 3338541 | 3342892 | 4351 | Present in 0157:[NAME], absent in UPEC CFT073, fatty acid degradation cluster, deletion in UPEC CFT073 to create gene fusion
ROD48 | 3387178 | 3441699 | 54521 | Genomic island 2. Sequence divergence between 0157:[NAME] and UPEC CFT073 strains, carries putative sulfatase and Tia homologue-epithelial adherence and invasion protein, helicase, plasmid replication proteins, hypothetical protein, exported/membrane proteins, bacteriocin biosynthesis-also may have a role in siderophore production, putative acetyltransferase)
ROD49 | 3442891 | 3499011 | 56120 | Partial present in UPEC CFT073, absent in 0157:[NAME], [NAME]. island, capsule cluster, type II secretion system, accessory colonization factor AcfD , glycolate catabolism cluster, [NAME]. secondary metabolism(?)
ROD50 | 3550689 | 3553906 | 3217 | Present in UPEC CFT073, absent in 0157:[NAME], islet (arylsulfotransferase and Disulfide bond formation proteins, dsbl and dsbI)
ROD51 | 3556421 | 3561395 | 4974 | Fimbrial operon 9. Present in UPEC CFT073, absent in 0157:[NAME], fimbrial usher genes
ROD52 | 3846177 | 3851050 | 4873 | Present in 0157:[NAME], absent in UPEC CFT073, fructoselysine utilization operon (transporter, regulator, enzymes)
ROD53 | 3851158 | 3858567 | 7409 | Present in UPEC CFT073, absent in 0157:[NAME], [NAME]. metabolism (contains phosphotriesterase family protein)
ROD54 | 3910346 | 3917538 | 7192 | Fimbrial operon 10. Sequence divergence between 0157:[NAME] and UPEC CFT073 strains
ROD55 | 3964269 | 3979285 | 15016 | Present in 0157:[NAME], absent in UPEC CFT073, [NAME]. secondary metaoblism (fatty acid like?)
ROD56 | 4013854 | 4020056 | 6202 | Partially present in 0157:[NAME] and UPEC CFT073, arsenical resistance cluster (region deleted in other E. coli, 042 contains extra arsD and arsA)
ROD57 | 4122431 | 4130479 | 8048 | Partial present in UPEC CFT073, absent in 0157:[NAME], [NAME]. carbohydrate catabolism (regulator, transporter, enzymes including: 3-keto-L-gulonate 6-phosphate decarboxylase, 3-epimerase, L-xylulose kinase)
ROD58 | 4130511 | 4138689 | 8178 | Present in 0157:[NAME], absent in UPEC CFT073, misc transport islet (regulators, transporter
ROD59 | 4180349 | 4185521 | 5172 | Present in 0157:[NAME], divergent in UPEC CFT073, LPS biosynthetesis genes, orthologous replacement
ROD60 | 4198051 | 4218142 | 20091 | prophage 7. Unique to 042 (hypothetical protein, prophage maintenance system killer protein)
ROD61 | 4236703 | 4247732 | 11029 | prophage-like. Sequence divergence between 0157:[NAME] and UPEC CFT073 strains (various phage proteins, amber mutation-suppressing protein, DNA primase), inserted at tRNA, flanked by repeats
ROD62 | 4252237 | 4270691 | 18454 | Unique to 042, pathogenicity island (homologues of salmonella invasin chaperone, sicA; cell invasion protein, SipB; cell invasion protein, SipD; transcriptional regulator, HilA; large repetative protein-possible invasin)
ROD63 | 4294718 | 4299559 | 4841 | Present in 0157:[NAME], absent in UPEC CFT073, [NAME]. sugar uptake operon (regulator, PTS protein and 6-phospho-beta-glucosidase)
ROD64 | 4305381 | 4310103 | 4722 | Present in UPEC CFT073, absent in 0157:[NAME], galactonate utilization operon
ROD65 | 4334993 | 4341871 | 6878 | Present in 0157:[NAME], divergent in UPEC CFT073, [NAME]. proteins
ROD66 | 4347120 | 4377180 | 30060 | Absent in UPEC CFT073, divergent in 0157:[NAME], putative composite island containing integron (?), (fimbrial usher genes, chloramphenicol acteyl transferase, transposase, Streptomycin adenyltransferase, thidium bromide resistance protein, mercuric resistance operon, tetracycline resistance), IS element repeats flank integron
ROD67 | 4460088 | 4465851 | 5763 | Unique to 042, islet, exported proteins
ROD68 | 4535650 | 4548272 | 12622 | Present in 0157:[NAME], absent in UPEC CFT073, sugar transport and utilization operon
[NAME] | 4831528 | 4948803 | 117275 | Genomic island 3. prophage-related. Absent in 0157:[NAME], divergent in UPEC CFT073, inserted at tRNA, flanked by repeats
ROD70 | 4995917 | 5000899 | 4982 | Unique to 042, islet, [NAME]. utilization (regulator, transporter, enzymes)
ROD71 | 5063137 | 5067364 | 4227 | Present in 0157:[NAME], divergent in UPEC CFT073, [NAME]. metabolism (regulator, hypothetical proteins, oxidoreductase)
ROD72 | 5081503 | 5162329 | 80826 | Divergent in 0157:[NAME] and UPEC CFT073, pathogenicity island, similarity to plasmid bourne proteins, (signal transduction protein, [NAME] regulator, PTS transporter, Major Facilitator Superfamily protein, DeoR regulator, putative choline transporter, LPS biosynthesis protein, VirK-required for proper localization of icsa (virg) at the surface of Shigella, glycosyl transferase, Fec iron(iii) dicitrate transport transport system, including fecR and fecI, aemolysin expression modulating protein, pertactin-domain autotransporter protein, ntirestriction protein, helicase, putative restriction system proteins), posible composite with insertion of island witin unique region, island inserted at a tRNA and is flanked by repeats