TABLE 2.
Homologies of the pathogen-specific clones
| Clone | Length (kb) | Positiona | Homology of ORFb | BLASTX significance | Inter- or intragenic | Accession no. | Reference |
|---|---|---|---|---|---|---|---|
| Virulence-associated genes | |||||||
| Bm033 | 304 | 0.28 and 0.6 | PilC1 (pilus-associated protein), N. meningitidis (Y13020) | 0 | Coding | AF169442 | 38 |
| Bm007 | 204 | PilC1 | Coding | AF169438 | |||
| Cm018 | 276 | PilC1 | Coding | AF169446 | |||
| Cm101 | 585 | PilC1 | Coding | AF169457 | |||
| Cm024 | 600 | 0.45 | Ssa1 (serotype-specific antigen), Pasteurella haemolytica (U07788) | 1e-7 | Coding | AF169448 | 18 |
| Em085 | 286 | Ssa1 | Coding | AF169473 | |||
| Em005 | 171 | 0.67 | YgiY (putative sensor/kinase protien), E. coli (P40719) | 2e-26 | Coding | AF169461 | 6 |
| IrlS (two-component regulatory system protein) Burkholderia pseudomallei (AF005358) | 4e-19 | 24 | |||||
| Cg014 | 156 | 0.85 | Iga (IgA protease), Neisseria gonorrhoeae (X04835) | 0 | Coding | AF169423 | 36 |
| Cm122 | 311 | Iga | Coding | AF169458 | |||
| Em033 | 276 | Iga | Coding | AF169466 | |||
| Bg021 | 444 | 1.55 | AidA-1 (putative adhesin), E. coli (D90793) | 2e-23 | Coding/inergenic | AF169420 | 1 |
| VirG (virulence-associated protein), Shigella flexnerii (M22802) | 4e-23 | 32 | |||||
| Eg008 | 302 | 1.9 | HlyIII (hemolysin III.), Bacillus cereus (P54176) | 3e-25 | Coding/intergenic | AF169427 | 4 |
| DNA modification, phage-related, and insertion sequences | |||||||
| Eg016 | 326 | 0.18 | DcmH (cytosine-specific methyltransferase), N. gonorrhoeae (AF001598) | 1e-148 | Coding | AF169431 | 20 |
| Cm130 | 851 | 0.42 | HgiDIIM (cytosine-specific methyltransferase), Herpetosyphon giganteus (JT0594) | 7e-49 | Coding | AF169459 | 13 |
| Em024 | 271 | HgiDIIM | Coding | AF169464 | |||
| Eg010 | 271 | HgiDIIM | Coding | AF169428 | |||
| Cm040 | 269 | HgiDIIM | Coding/intergenic | AF169451 | |||
| Em029 | 268 | 0.45 | Transposase in insertion sequence, Aeromonas salmonicida (L27157) | 1e-10 | Coding/intergenic | AF169465 | 21 |
| Cm016 | 280 | 1.17 | Hypothetical protein in insertion sequence IS150-like, N. gonorrhoeae (L36381) | 2e-88 | Coding | AF169445 | 37 |
| Cm042 | 203 | 1.75 | Hypothetical protein phage Cf1c), Xanthomonas campestris (M57538) | 1e-19 | Coding | AF169452 | 31 |
| Eg003 | 364 | 1.95 | RstA2 (phage CTX), Vibrio cholerae (U83796) | 7e-8 | Coding | AF169426 | 45 |
| Cg011 | 315 | Multiple | ORF1 (transposase, insertion sequence IS1106 (partial; DNA homology), N. meningitidis | - | Coding/intergenic | AF169422 | 28 |
| Cm034 | 381 | Multiple | Insertion sequence IS1016, Haemophilus influenzae (X58176) | 4e-10 | ? | AF169450 | 30 |
| Cg004 | 358 | Multiple | Hypothetical transposase, Synechocystis sp. (D90913, g1653459) | 2e-18 | Coding/intergenic | AF169421 | 25 |
| Em034 | (365)c | Multiple | Correia repetitive element (partial; DNA homology), N. gonorrhoeae (M19676) | 8e-80 | Coding/intergenic | AF169467 | 8 |
| Metabolic and transporter genes | |||||||
| Bg012 | 363 | 0.7 | CvaB (ATP-binding colicin secretion protein), E. coli (U47048) | 8e-16 | Coding | AF169419 | 17 |
| Bm026 | 181 | 0.7 | GluP (glucose/galactose transporter), Brucella abortus (Q44623) | 1e-104 | Coding | AF169441 | 14 |
| Eg028 | 251 | 1.22 | Ggt (γ-glutamyltranspeptidase), Bacillus subtilis (P54422) | 2e-9 | Coding | AF169435 | 48 |
| Bm003 | (360)c | 1.6 | PorA (class 1 porin), N. meningitidis | 0 | Coding | AF169437 | 5 |
| Bg004 | 363 | PorA | Coding | AF169417 | |||
| Cm029 | 248 | 2.0 | SpeA1 (arginine decarboxylase), E. coli (M31770) | 1e-138 | Coding | AF169449 | 34 |
| Bm011 | 347 | SpeA1 | Coding | AF169439 | |||
| Eg022 | 281 | SpeA1 | Coding/intergenic | AF169433 | |||
| Em061 | 261 | SpeB (agmatinase), E. coli (M32363) | 1e-134 | Coding | AF169470 | 43 | |
| Cm062 | 212 | 2.0 | YflS (hypothetical protein), B. subtilis (D86417, g2443241) | 1e-130 | Coding | AF169456 | 49 |
| SODiT1 (dicarboxylate translocator), Spinacia oleracea (U13238) | 3e-97 | 46 | |||||
| Eg040 | 276 | 2.04 | CppM (putative CPEP phosphomutase), E. coli (P77541) | 8e-91 | Coding | AF169436 | 12 |
| Em078 | 308 | CisZ (citrate synthase), E. coli (P31660) | 8e-28 | Coding | AF169472 | 35 | |
| Cm047 | 224 | CisZ | Coding | AF169455 | |||
| Genes of unknown function | |||||||
| Cg023 | 470 | 2.0 | Hypothetical protein ‘ORF1’, N. meningitidis (AJ010115) | 6e-23 | Coding | AF169425 | 47 |
| Em103 | (375)c | 2.04 | HI1005 (hypothetical protein), H. influenzae (U32781) | 3e-56 | Coding | AF169476 | 16 |
| Cm045 | 206 | HI1005 | Coding | AF169454 | |||
| Cg015 | 267 | HI1005 | Coding | AF169424 | |||
| Em023 | 273 | HI1005 | Coding | AF169463 | |||
| Em094 | 196 | 2.04 | Ycb9 (hypothetical protein), Pseudomonas denitrificans | 6e-9 | Coding | AF169475 | 9 |
| Bm040 | 243 | 2.04 | YraM (hypothetical protein), Bacillus subtilis (U93875, g1934631) | 1e-50 | Coding | AF169443 | 42 |
| Em059 | (515)c | YraM | Coding | AF169469 | |||
| Genes with no homologies | |||||||
| Em110 | 217 | 0.6 | None | Coding | AF169477 | ||
| Bm013 | 349 | None | Coding | AF169440 | |||
| Cm043 | 229 | None | Coding | AF169453 | |||
| Bg007 | 400 | None | Coding | AF169418 | |||
| Em045 | 260 | None | ? | AF169468 | |||
| Em070 | 323 | 0.6 | ? | AF169471 | |||
| Em087 | 238 | 0.7 | None | Coding | AF169474 | ||
| Eg014 | 293 | 1.75 | None | Intergenic | AF169430 | ||
| Cm008 | 236 | 2.05 | None | Coding | AF169444 | ||
| Eg012 | 309 | None | Coding | AF169429 | |||
| Em002 | 308 | None | Coding | AF169460 | |||
| Cm020 | 354 | 2.25 | None | Coding | AF169447 | ||
| Eg024 | 345 | None | Coding | AF169434 | |||
| Em022 | (305)c | Multiple | None | ? | AF169462 |
a
Positions were determined by comparison of the pattern of reactivity on Southern blots with those of the macrorestriction map of N. meningitidis Z2491 (11) and by analysis of contigs from the genome-sequencing projects which contained the clones. The position is given in megabases, according to reference 11.
b
Homologous proteins or ORFs are those giving the best BLASTX scores, using the corresponding ORF or intergenic region as query sequence.
c
Sizes of clones in parentheses are approximate, where the sequence information was not considered sufficiently reliable to give an exact number of bases.