TABLE 1.

Specific SSH fragments and their homologies determined with the BLASTN and BLASTX algorithmsa

Sequence group and cloneHomology by BLASTN or BLASTXLength (bp)e valueGenBank accession no.Function
Virulence-related sequences
    O2-38 Shigella flexneri 2a strain 301 SF30025960.0 AAN44483 Predicted ATP-binding protein involved in virulence
    O2-106 E. coli O157:H7 EDL933 eivA3005e−90 AAG57987 Type III secretion apparatus protein
    O2-108 S. flexneri 2a strain, sit operon5300.0 AAN42967-9 Iron transport proteins
    O2-154 E. coli pSFO157 SfpD392e−124 AJ131667 P pilus assembly chaperon
    O78-13 E. coli strain 536 PAI III sfaG6170.0 CAA34652 Minor subunit of AC/I pili
    O78-74 E. coli CFT073 sfaH8170.0 NP_753159 Minor subunit of AC/I pili
    O78-44 + O78-102 E. coli strain 536 PAI III6310.0 X16664 Enterobactin receptor iroN
    O78-95 E. coli O157:H71,0020.0 NP_290185 Autotransporter, putative adhesin
    O78-96 Yersinia pestis ybtS 6660.0 NP_405477 Versiniabactin synthesis
    O78-163 E. coli O157:H7 eivC6220.0 NP_289427 Type III secretion system
Known and putative functions
    O2-4 Shewanella oneidensis MR-12993e−49b NP_716453 Outer membrane efflux family protein
    O2-16 S. flexneri 2a SRL PAI3145e−72 AF326777 LysR-like transcriptional regulator
    O2-23 S. enterica serovar Typhimurium genomic island I S005591e−109 AF261825 Putative mating pair stabilization protein
    O2-27 E. coli clone SauE4 C12, neonatal meningitis strain-specific DNA sequence6361e−58 AF222135 Putative Lon protease, truncated
    O2-37 S. flexneri 2a she PAI ORF24 + ORF255530.0 AAK00478 , AAK00479ORF24, putative antirestriction protein
ORF25, putative RadC-like protein YeeS
    O2-54 E. coli beta-lactamase5190.0 AF427132 Beta-lactamase
    O2-60 E. coli cvaB 4730.0 X57524 Protein involved in colicin V secretion
    O2-64 Staphylococcus aureus subsp. MW02184931e−10c BAB94083 Maltose- and glucose-specific factor II
    O2-113 E. coli CFT073 c4764277e−104 AE016769 AE014075 Carbamate kinase-like protein YahI
    O2-173 E. coli hsdS 5761e−27 AJ132566 Subunit of restriction enzyme
    O2-284 E. coli O157:H7 EDL933 Z25084100.0 AAG56520 Putative efflux pump
    O2-316 S. flexneri 2a strain SF27633910.0 AE015290 , AE005674Putative transcriptional regulator protein
    O2-318 Sulfolobus solfataricus 2630.003c AAK4183 Glycosyltransferase
    O2-323 Vibrio cholerae traV 5479e−31c AAL59672 Sex pilus assembly
    O2-333 S. enterica serovar Typhimurium LT2 STM23424523e−65 AE008805 , AE006468Putative inner membrane and transport protein
    O78-12 E. coli strain 536 PAI III ORF381,4730.0 CAD66186 Putative nitrile hydratase
    O78-73a E. coli CFT0735970.0 NP_753855 Putative regulator
    O78-73b E. coli CFT0737040.0 NP_753853 Putative enzyme
    O78-84 Legionella pneumophila 5168e−28c AAM08232 Putative type I restriction enzyme
    O78-151 S. flexneri 2a strain 301 SHE PAI5720.0 NP_708769 Putative antirestriction protein
    O78-169b S. enterica serovar Typhi6e−38c NP_457351 Putative regulator
Unknown function and no homology
    O2-1 E. coli strain 536 PAI II ORF44367e−135 CAD42059 Conserved hypothetical protein
    O2-14766
    O2-32 Silicibacter pomeroyi 2953e−49bUnknown
    O2-42 E. coli O157:H7 EDL933, Z16374633e−40 NP_309406 Conserved hypothetical protein
    O2-87 S. pomeroyi 3226e−07bUnknown
    O2-125804
    O2-132545
    O2-138 E. coli strain 536 PAI II, no ORF2222e−43 AJ494981 Unknown
    O2-144197
    O2-157518
    O2-158 Klebsiella pneumoniae plasmid, no ORF5303e-59 AJ276453 Unknown
    O2-164262
    O2-165 Photorhabdus luminescens strain NC19 NgrC3394e−91 AAK16082 Unknown
    O2-193491
    O2-207 E. coli CFT073 c2499274e−148 AAN80955 Conserved hypothetical protein
    O2-210 E. coli strain 536 PAI I, ORF28 + ORF29422e−174 CAD33738 CAD33739 Conserved hypothetical proteins
CAD33739
    O2-280153
    O2-311 E. coli strain 536 PAI I, no ORF3045e−13 AJ488511 Unknown
    O2-319425
    O2-334295
    O2-345 E. coli CFT073, no ORF912e−43 AE016770 AE014075 Unknown
AE014075
    O2-349 E. coli strain 536 PAI I ORF731838e−91 AJ488511 Putative intergenic-region protein
    O2-353 E. coli O157:H7 EDL933 Z1600365e−125 AE005309 AE005174 Hypothetical protein
AE005174
    O2-355 Pseudomonas resinovorans 4452e−15c BAC41652Hypothetical protein
    O78-17 E. coli O157:H7, O island 78900.0 AE005199 Hypothetical protein
    O78-18 E. coli O157:H7, O island 76590.0 AE005198 Conserved hypothetical protein
    O78-24634
    O78-27a S. flexneri 2A strain 301, no ORF1,3380.0 AE015221 Unknown
    O78-55602
    O78-63 E. coli O157:H76040.0 NP_310823 Hypothetical protein
    O78-69665
    O78-79 Pseudomonas syringae 7578e−08c NP_791901 Hypothetical protein
    O78-138375
    O78-161 E. coli plasmid p1658/97 ORF508370.0 AAO49623 Putative protein
  • a Homology was determined with the BLASTN or BLASTX algorithm.

  • b Microbial blast e value.

  • c BLASTX e value.