Table 2.

The ORFs in SGI1 DNA whose putative products exhibit significant homologya to extant protein sequences

ORFbLocationc(start–stop)Size in:% G+CE valued% Identity/rangeeExhibits homology to (accession no. and/or reference):
S001 int 367–15841,218405431.0e-4029/365Integrase from Tn4555; Bacteroides fragilis (U75371)
S002 xis 1949–158136912246.14.0e-0531/94Excisionase from Tn4555; B. fragilis (U75371)
S003 rep 3260–230795431744.47.0e-4334/277Replication protein RepA pMG101; Rhodopseudomonas palustris (AB031076)
S0056384–36252,760919462.0e-5224/862Mating pair stabilization protein TrhN, plasmid R27; serovar Typhi (AF105019)
S0067014–648153417743.80.0125/159Flagellar transcriptional activator Fr1B; Bordetella bronchiseptica(U17998)
S011 trhG 11992–85883,4051,13445.52.0e-2721/822Pilus assembly protein, plasmid R27; serovar Typhi (AF250878)
S012 trhH 13420–119961,42547443.22.0e-3326/446Pilus assembly protein TrhH, plasmid R27; serovar Typhi (AF112468)
S02017712–16747966321532.0e-2128/321Orf3 protein, putative integrase, pFNL10; Francisella tularensis(AF121418)
S02320328–186881,64154647.15.0e-2024/448DNA helicase II UvrD; Haemophilus influenzae (U32798)
S02422271–203461,92664146.42.0e-0522/468Overcoming lysogenization defect protein OLD, exonuclease; bacteriophage P2 (AF063097)
S02524892–223492,54484738.96.0e-1524/416Hypothetical protein Y4bN, symbiosis plasmid; Rhizobium sp. NGR234 (AE000066)
S02625902–2491399032939.21.0e-4132/330ATPase Y4kL, symbiosis plasmid; Rhizobium sp. NGR234 (AE000081)
S027 tnpR 26565–2598158519446.80100/171Resolvase (3, 5)
S028 int1 27852–268391,01433761.20100/193Integrase of class I integrons (3, 5, 29)
S029 aadA2 27998–2878979226351.90100/263Spectinomycin/streptomycin resistance protein (3, 5, 29)
S030 qacEΔ128953–29300348115500100/115Quaternary ammonium compound and disinfectant resistance partial protein (3, 5,29)
S031 sulIΔ129294–2982152817663.10100/176Sulfonamide resistance partial protein (3, 5, 29)
S032 floR 30482–316961,21540458.20100/404Chloramphenicol and florfenicol resistance (3, 5)
S033 tetR 32529–3190362720859.20100/209Tetracycline resistance regulator; repressor (3, 5)
S034 tet(G)32681–338081,12837557.50100/375Tetracycline resistance (3, 5)
S035 orf1 33829–3462079226361.64.0e-2535/194LysR-type transcriptional regulator; Deinococcus radiodurans (5)
S036 orf2 36196–347121,48249468.93.0e-9058/484Putative transposase OrfA, plasmid 10507-1, E. coli (5)
S037 groEL/intI 37124–3647165421763.30100/217GroEL-like/integrase fusion protein (5)
S038 pse-1 37330–38196867288410100/288Carpencillinase (3, 5, 29)
S039 qacEΔ138413–38760348115500100/115Quaternary ammonium compound and disinfectant resistance partial protein (3, 5,29)
S040 sulI 38754–3959384027961.70100/279Sulfonamide resistance (3, 4, 5, 29)
S041 orf5 39721–4022150116665.10100/166Putative acetyltransferase in Tn21 (4)
S042 orf6 40245–405322889560.80100/95Hypothetical protein in pSCH884 integron In5 (4)
S043 tnpA 40698–41492795264610100/264Transposase from IS6100 (4)
  • a Significant homology is defined as an E value of ≤1e-05 and/or >20% identity over at least 60% of the length of the protein.

  • b ORFs of at least 180 bp (≥60 amino acids). Named ORFs are based on those previously characterized or designated here based on a putative function.

  • c Nucleotide position in the sequence deposited under accession no. AH261825.

  • d Expect value. Values of 0.0 were as returned by BLAST.

  • e % Identity as returned by BLAST search and range (number of amino acids and gaps) over which identity value was calculated.