Table 2.

Homologies of the pathogen-specific clones

CloneLength (kb)PositionaHomology of ORFbBLASTX significanceInter- or intragenicAccession no.Reference
Virulence-associated genes
 Bm0333040.28 and 0.6PilC1 (pilus-associated protein),N. meningitidis(Y13020)0Coding AF169442 38
 Bm007204PilC1Coding AF169438
 Cm018276PilC1Coding AF169446
 Cm101585PilC1Coding AF169457
 Cm0246000.45Ssa1 (serotype-specific antigen), Pasteurella haemolytica(U07788)1e-7Coding AF169448 18
 Em085286Ssa1Coding AF169473
 Em0051710.67YgiY (putative sensor/kinase protien), E. coli(P40719)2e-26Coding AF169461 6
IrlS (two-component regulatory system protein)Burkholderia pseudomallei(AF005358)4e-19 24
 Cg0141560.85Iga (IgA protease),Neisseria gonorrhoeae(X04835)0Coding AF169423 36
 Cm122311IgaCoding AF169458
 Em033276IgaCoding AF169466
 Bg0214441.55AidA-1 (putative adhesin),E. coli(D90793)2e-23Coding/inergenic AF169420 1
VirG (virulence-associated protein), Shigella flexnerii (M22802)4e-23 32
 Eg0083021.9HlyIII (hemolysin III.),Bacillus cereus(P54176)3e-25Coding/intergenic AF169427 4
DNA modification, phage-related, and insertion sequences
 Eg0163260.18DcmH (cytosine-specific methyltransferase), N. gonorrhoeae(AF001598)1e-148Coding AF169431 20
 Cm1308510.42HgiDIIM (cytosine-specific methyltransferase), Herpetosyphon giganteus(JT0594)7e-49Coding AF169459 13
 Em024271HgiDIIMCoding AF169464
 Eg010271HgiDIIMCoding AF169428
 Cm040269HgiDIIMCoding/intergenic AF169451
 Em0292680.45Transposase in insertion sequence, Aeromonas salmonicida(L27157)1e-10Coding/intergenic AF169465 21
 Cm0162801.17Hypothetical protein in insertion sequence IS150-like, N. gonorrhoeae(L36381)2e-88Coding AF169445 37
 Cm0422031.75Hypothetical protein phage Cf1c), Xanthomonas campestris(M57538)1e-19Coding AF169452 31
 Eg0033641.95RstA2 (phage CTX), Vibrio cholerae(U83796)7e-8Coding AF169426 45
 Cg011315MultipleORF1 (transposase, insertion sequence IS1106 (partial; DNA homology), N. meningitidis -Coding/intergenic AF169422 28
 Cm034381MultipleInsertion sequence IS1016, Haemophilus influenzae(X58176)4e-10? AF169450 30
 Cg004358MultipleHypothetical transposase,Synechocystis sp. (D90913, g1653459)2e-18Coding/intergenic AF169421 25
 Em034(365)c MultipleCorreia repetitive element (partial; DNA homology), N. gonorrhoeae(M19676)8e-80Coding/intergenic AF169467 8
Metabolic and transporter genes
 Bg0123630.7CvaB (ATP-binding colicin secretion protein), E. coli(U47048)8e-16Coding AF169419 17
 Bm0261810.7GluP (glucose/galactose transporter), Brucella abortus(Q44623)1e-104Coding AF169441 14
 Eg0282511.22Ggt (γ-glutamyltranspeptidase),Bacillus subtilis(P54422)2e-9Coding AF169435 48
 Bm003(360)c 1.6PorA (class 1 porin), N. meningitidis 0Coding AF169437 5
 Bg004363PorACoding AF169417
 Cm0292482.0SpeA1 (arginine decarboxylase), E. coli(M31770)1e-138Coding AF169449 34
 Bm011347SpeA1Coding AF169439
 Eg022281SpeA1Coding/intergenic AF169433
 Em061261SpeB (agmatinase), E. coli(M32363)1e-134Coding AF169470 43
 Cm0622122.0YflS (hypothetical protein),B. subtilis (D86417, g2443241)1e-130Coding AF169456 49
SODiT1 (dicarboxylate translocator), Spinacia oleracea (U13238)3e-97 46
 Eg0402762.04CppM (putative CPEP phosphomutase), E. coli(P77541)8e-91Coding AF169436 12
 Em078308CisZ (citrate synthase), E. coli(P31660)8e-28Coding AF169472 35
 Cm047224CisZCoding AF169455
Genes of unknown function
 Cg0234702.0Hypothetical protein ‘ORF1’, N. meningitidis(AJ010115)6e-23Coding AF169425 47
 Em103(375)c 2.04HI1005 (hypothetical protein), H. influenzae(U32781)3e-56Coding AF169476 16
 Cm045206HI1005Coding AF169454
 Cg015267HI1005Coding AF169424
 Em023273HI1005Coding AF169463
 Em0941962.04Ycb9 (hypothetical protein),Pseudomonas denitrificans 6e-9Coding AF169475 9
 Bm0402432.04YraM (hypothetical protein),Bacillus subtilis (U93875, g1934631)1e-50Coding AF169443 42
 Em059(515)c YraMCoding AF169469
Genes with no homologies
 Em1102170.6NoneCoding AF169477
 Bm013349NoneCoding AF169440
 Cm043229NoneCoding AF169453
 Bg007400NoneCoding AF169418
 Em045260None? AF169468
 Em0703230.6? AF169471
 Em0872380.7NoneCoding AF169474
 Eg0142931.75NoneIntergenic AF169430
 Cm0082362.05NoneCoding AF169444
 Eg012309NoneCoding AF169429
 Em002308NoneCoding AF169460
 Cm0203542.25NoneCoding AF169447
 Eg024345NoneCoding AF169434
 Em022(305)c MultipleNone? 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.