Table 1.

Summary of BLAST search of clones that were specific forE. coli strain C5 and had significant homologiesa

ClonebInsert size (bp)Sequence(s) with similaritycScoreProbabilityGenBank accession no.
SauE15.A1163IS629(N), plasmid pO157, E. coliO157:H7315 e −84 AB011549
SauE15.A7190 iroC (N), ATP cassette transporter (iron-regulated locus), Salmonella enterica serovar Typhi157 e −37 U6129
SauE15.B2294 repB (N); replication protein, plasmid pCD1; Yersinia pestis 123 e −26 AF053946
SauE15.B6157 kps (N), promoter region of polysialic acid gene cluster region 3, E. coli 242 e −62 U05251
SauE15.B9107 traD (N), F sex factor plasmid,E. coli 198 e −50 M29254
SauE15.B10240ORF 34 and 35 (P), 102-kb unstable region, Y. pestis 69 e −12 CAA21357
SauE15.B12479unknown protein (P), E. coli ec11 102 e −21 AF044503
SauE15.C1100 r6 (N), transposase, pathogenicity island of E. coliCFT073198 e −49 AF081285
SauE15.C6119IS100 (N), Y. pestis 228 e −58 L19030
SauE15.C7155TonB-dependent receptor HI1217 precursor (P),Haemophilus influenzae 52 e −7 P45114
SauE15.C9273 rhuM (N), pathogenicity island of Salmonella enterica serovar Typhimurium (SPI3)311 e −83 AF106566
SauE15.C1177 orfE (N); promoter-distal region of the tra operon, plasmid R100; S. flexneri 129 e −29 X55815
SauE15.D4153IS100 (N), Y. pestis 287 e −76 L19030
SauE15.D8347 r3 (N), beta-cystathionase, pathogenicity island of E. coliCFT073615 e −174 AF081286
SauE15.E4281 senB (N), enterotoxin, E. coli 541 e −152 Z54195
SauE15.E11314 traJ, Y (N), plasmid R1–19, E. coli 523 e −147 M19710
SauE15.F3422 chuA (P), heme utilization gene,E. coliO157:H798 e −20 U67920
SauE15.F9137Thioesterase (P), Bacillussp.48 e −6 AB016427
SauE15.F10210 r3 (N), beta-cystathionase, pathogenicity island of E. coliCFT073408 e −112 AF081286
SauE15.G3206 traG (N), plasmid R100, S. flexneri 165 e −39 U01159
SauE15.G6328IS100 (N), Y. pestis 480 e −134 L19030
SauE15.H5200HMWP1 protein (P), Yersinia enterocolitica 80 e −15 CAA73127
SauE15.H7150Oxydoreductase (P), Thermotoga maritima 160 e −11 AE001762
SauE15.H10141 traT (N), plasmid R100, E. coli 280 e −74 J01769
SauE15.H11160Hemoglobin protease (P), E. coliEB150 e −6 CAA11507
SauE15.I3176 asst (N), arylsulfate sulfotransferase, Klebsiellasp.341 e −92 U32616
SauE15.I11162 chuA (N), heme utilization gene,E. coliO157:H7305 e −82 U67920
SauE15.J7118 iroB (N), glucosyl transferase homolog, Salmonella serovar Typhi74 e −12 U62129
SauE15.J996IS100 (N), Y. pestis 174 e −42 L19030
SauE15.M4193 r3 and malX (N), pathogenicity island of E. coliCFT073383 e −104 AF081286
SauE15.M8149Delta-(l-α-aminoadipyl)-l-cyteinyl-d-valine synthetase (P), Penicilliumsp.65 e −11 P26046
SauE15.M12119 senB (N), enterotoxin of enteroinvasive E. coli 228 e −58 Z54195
SauE15.N7188Plasmid pColBM-C1139 (N), E. coli 208 e −52 M35683
SauE4.A2321ORF 36 (N), 102-kb unstable region, Y. pestis 135 e −30 AL031866
SauE4.A5249 r3 (N), beta-cystathionase, pathogenicity island of E. coliCTF073355 e −96 AF081286
SauE4.B4360IS200 (N), E. coli 523 e −147 L25845
SauE4.C7275Hippurate hydrolase (P), Campylobacter jejuni 54 e −7 P45493
SauE4.C11255Pristinamycine I synthase (P),Streptomycesspp.51 e −6 CAA67248
SauE4.D3239 hlyB (N), hemolysine, E. coli 474 e −132 M81823
SauE4.E3263 shuX genes (N), heme utilization genes, Shigella dysenteriae 387 e −106 U64516
SauE4.E11242IS66 (N), E. coli 329 e −88 AF119170
SauE4.F8188 sorC genes (N), sor operon for l-sorbose utilization, Klebsiella pneumoniae 139 e −31 X66059
SauE4.F9439YfkN (P), Bacillus subtilis 57 e −8 BAA23404
SauE4.F12324 kpsM (N), polysialic acid gene cluster region 3, E. coliK16420 M57382
SauE4.H285 sorM (N), sor operon forl-sorbose utilization, K. pneumoniae 105 e −22 X66059
SauE4.I2431 yihA (N), plasmid R100,S. flexneri 8290 AP000342
TspE4.A5271 pap and prsK (N), P-pili protein, E. coli 498 e −139 X61239
TspE4.A8216ORF 17 kD of prs pili operon (N), cytoplasmic protein, E. coli 387 e −106 X61238
TspE4.A9179 kpsT (N), polysialic acid gene cluster region 3, E. coliK1347 e −94 M57381
TspE4.A10212HecB (P), putative hemolysin activator transporter, Erwinia chrysanthemi 73 e −13 AAC31980
TspE4.B1229 r1 (N), pathogenicity island of E. coliCFT073430 e −119 AF081286
TspE4.B5215Sensory transduction histidine kinase (P),Synechocystissp.52 e −7 BAA18223
TspE4.B9319 senB (N), enterotoxin of enteroinvasive E. coli 617 e −175 Z54195
TspE4.B12430IS100 (N), Y. pestis 6980 L19030
TspE4.C10267Intergenic K42 capsule cluster (N), E. coli 466 e −129 AF118251
TspE4.D2232 waaL (N), lipid A core-to-surface polymer ligase, E. coli 404 e −111 AF019746
TspE4.D4245ORF 169 (N), plasmid F, E. coli 456 e −126 X17539
TspE4.D10222 cnf1 (N), cytotoxic necrotizing factor, E. coli 440 e −122 X70670
TspE4.D11217 hlyB (N), hemolysin, E. coli 422 e −117 M81823
TspE4.E3298 hlyD (N), hemolysin, E. coli 553 e −156 M10133
TspE4.E4267ORF 95 (N), plasmid F, E. coli 482 e −134 X17539
TspE4.E6190 l-sorbose P reductase (P), K. pneumoniae 112 e −25 P37084
TspE4.E8285 hlyB (N), hemolysin, E. coli 541 e −152 M81823
TspE4.G7238 tra (N), plasmid F, E. coli 448 e −124 X61575
TspE4.G8323Transmembrane protein (P), E. coli 82 e −15 AAA92620
TspE4.H1283Arginine deiminase (P), Pseudomonas aeruginosa 63 e −10 P13981
TspE4.H9179 traT (N), plasmid R100, E. coli 353 e −96 J01769
TspE4.H10223 prf and papI (N), adhesin regulatory gene, E. coli 418 e −115 X76613
TspE4.H11279ORF 9 (N), plasmid F, E. coli 456 e −127 X17539
TspE4.I10269 neuC (N), capsule gene cluster,E. coli 492 e −137 M84026
TspE4.J1327 yhtA (N), plasmid R100,E. coli 521 e −146 AP000342
TspE4.J6221 chuA (N), heme utilization gene,E. coliO157:H7375 e −102 U67920
TspE4.K3180 iss (N), serum survival, E. coli 270 e −70 AF042279
TspE4.K8184IS100 (N), E. coli 190 e −47 L19030
prf and papB (N), E. coli 143 e −32 X76613
TspE15.A1332Na+ H+ antiporter (P),H. influenzae 96 e −20 Q57007
TspE15.C1299 hra (N), heat-resistant agglutinin, E. coli99537 e −151 U07174
TspE15.C3386 hcp (N), E. coli 81 e −14 AF044503
TspE15.D7239Protein STBA (P), plasmid NR1, E. coli 87 e −17 P11904
TspE15.D9230 chuA (P), heme utilization gene,E. coliO157:H789 e −18 AAC44857
TspE15.E7360 kpsS (N), capsule gene cluster region 1, E. coliK5531 e −149 X74567
TspE15.G12287Putative amino transferase (P),B. subtilis 72 e −12 Q08432
TspE15.H2258Pyruvate formate lyase-activating enzyme (P),Streptococcus mutans 51 e −6 AAB89799
TspE15.H5310 cnf1 (N), cytotoxic necrotizing factor, E. coli 601 e −170 U42629
TspE15.H9273Major fimbrial subunit of F17-like fimbriae (P), E. coli 48 e −5 I41206
TspE15.I2112 prs and papE (N), P-pili protein, E. coli 222 e −57 X62158
  • a Only homologies with at least probability of e−5 were retained. Homologies to bacteriophages (n = 21) are not shown.

  • b Clones are designated by the name of the enzyme (Sau or Tsp), followed by the name of the strain used for the subtraction (E4 or E15) and a code composed of a letter and a number.

  • c The name of the gene sequence is given (with similarity type in parentheses), followed by the product or function that is encoded by the gene and/or the gene's location, as well as the organism name. N, similarity at the nucleotide level; P, similarity at the protein level; ORF, open reading frame.