Table 3.
Features of J166-specific clones with significant database matches
| Clone* | GenBank accession no. | Homolog (protein); accession no.; blastx P(N) value | DNA match, strain 26695† | |
|---|---|---|---|---|
| R-M | ||||
| 1 | C2 | AF025968 | HsdS, HI0216, 4e−36; HP1383, 1e−20 | 110/116, HP1383 |
| 2 | F3 | AF025974 | HsdS, MJ0130, 2e−11 | 52/55, HP1383 |
| 3 | A3 | AF025965 | BcgIα, HP1472, 2e−17; BC, gbL17341, 2e−16 | None |
| 4 | H5 | AF025982 | BcgIα, HP1472, 3e−10; BcgIβ BC spQ07606, 2e−07 | 150/160, HP1472, and upstream |
| 5 | F7 | AF025975 | HpyI, DNA methyltransferase HP1208, 6e−05 | None |
| 6 | H4/F | AF025980 | DNA methyltransferase, M.AvaI, AV gbX98339, 1e−08 | None |
| H4/R | AF025981 | None | None | |
| 7 | F1 | AF025973 | StyLT1 DNA methyltransferase, spP40814, 9e−16 | 106/113, HP1369 |
| Possible metabolic | ||||
| 8 | E3 | AF025971 | l-Serine deaminase, HP0132; E. coli yhaE-like, gbU82664, 7e−05 | 93/96, HP0132, HP0133 |
| 9 | G7 | AF025978 | Hydrogenase expression, HP0047, 1e−21 | 116/122, HP0047 |
| Hypothetical protein homolog, function unknown | ||||
| 10 | D3 | AF025970 | Conserved HP0347, 4e−52; HP0338, 1e−54 | 231/249, HP0347; 142/155, HP0338 |
| 11 | H2 | AF025979 | Conserved HP0745, 6e−42 | 214/217, HP0745 |
| 12 | A7 | AF025966 | H. pylori HP0673, 2e−29 | 27/28, 68/80, HP0673 |
| 13 | G3 | AF025976 | H. pylori HP0594, 4e−06 | 110/114, HP0594 |
gb, GenBank; sp, Swiss-Prot; AV, Anabaena variabilis; BC, Bacillus coagulans; EC, Escherichia coli; HI, Haemophilus influenzae; HP, H. pylori; Sty, Salmonella typhimurium; MJ, Methanococcus jannaschii. Sequences of open reading frames designated HI, HP, and MJ (e.g., HI0216 and HP1383 for clone C2, line 1) are found using the genome-specific sections of the TIGR website.
Cloned DNAs ranged from 309 bp to 804 bp. They are arranged here according to putative functions, inferred from database matches. Clones with homology to R-M systems were subdivided into type I (clones C2, F3); type I-like (clones A3, H5; BcgI appears to be a type I-derived R-M enzyme (ref. 29; H. Kong, personal communication); type II (clones F7, H4); and type III (clone F1). J166-specific clones with no significant protein homology to current database entries were as follows: E7 (AF025972), which had a 59/62-bp match to the H. pylori genome sequence between HP0134 and HP0135; A1/F (AF025963) and A1/R (AF025964); B2 (AF025967); C8 (AF025969); and G4 (AF025977).
Extent of match (in bp) in longest stretch of sequence shared between J166-derived clone and the 26695 genome, based on sequence searches through the TIGR web site (http://www.tigr.org).