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Table 5. ORFs with high-density nucleotide polymorphisms*
|
Name |
Location |
Annotation |
|||
|
|
|
Function |
Lipo. |
Tran.§ |
Sig.ś |
|
BB0003 |
Main |
hypothetical protein |
|
+ |
|
|
BB0026 |
Main |
methylenetetrahydrofolate dehydrogenase |
|
+ |
|
|
BB0032 |
Main |
hypothetical protein |
|
+ |
+ |
|
BB0037 |
Main |
1-acyl-sn-glycerol-3-phosphate acyltransferase |
|
+ |
+ |
|
BB0082|| |
Main |
hypothetical protein |
|
|
|
|
BB0084 |
Main |
nifS protein |
|
+ |
|
|
BB0102 |
Main |
hypothetical protein |
|
|
|
|
BB0104 |
Main |
periplasmic serine protease |
|
+ |
|
|
BB0122 |
Main |
translation elongation factor |
|
|
|
|
BB0126 |
Main |
hypothetical protein |
|
+ |
+ |
|
BB0128 |
Main |
cytidylate kinase |
|
|
|
|
BB0144 |
Main |
glycine/betaine/L-proline ABC transporter, glycine/betaine/L-proline-binding protein |
+ |
+ |
+ |
|
BB0158 |
Main |
antigen, S2 |
|
+ |
+ |
|
BB0201 |
Main |
UDP-N-acetylmuramoylalanyl-D-glutamate--2,6-diaminopimelate ligase |
|
+ |
|
|
BB0218 |
Main |
phosphate ABC transporter, ATP-binding protein |
|
|
|
|
BB0225 |
Main |
hypothetical protein |
|
|
|
|
BB0236 |
Main |
hypothetical protein |
|
+ |
+ |
|
BB0251 |
Main |
leucyl-tRNA synthetase |
|
+ |
|
|
BB0276 |
Main |
flagellar biosynthesis protein |
|
+ |
+ |
|
BB0283 |
Main |
flagellar hook protein (flgE) |
|
|
|
|
BB0332 |
Main |
oligopeptide ABC transporter, permease protein (oppB-1) |
|
+ |
+ |
|
BB0344 |
Main |
DNA helicase (uvrD) |
|
|
|
|
BB0348 |
Main |
pyruvate kinase (pyk) |
|
+ |
|
|
BB0362 |
Main |
prolipoprotein diacylglyceryl transferase (lgt) |
|
+ |
|
|
BB0399 |
Main |
hypothetical protein |
|
+ |
+ |
|
BB0400 |
Main |
hypothetical protein |
|
|
|
|
BB0401 |
Main |
glutamate transporter |
|
+ |
+ |
|
BB0419 |
Main |
response regulatory protein (rrp-1) |
|
+ |
|
|
BB0438 |
Main |
DNA polymerase III, subunit beta (dnaN) |
|
|
|
|
BB0484 |
Main |
ribosomal protein S3 (rpsC) |
|
|
|
|
BB0492 |
Main |
ribosomal protein S8 (rpsH) |
|
|
|
|
BB0498 |
Main |
preprotein translocase subunit (secY) |
|
+ |
+ |
|
BB0502 |
Main |
DNA-directed RNA polymerase (rpoA) |
|
|
|
|
BB0512 |
Main |
hypothetical protein |
|
+ |
+ |
|
BB0550 |
Main |
flagellar protein (flaJ) |
|
|
|
|
BB0572 |
Main |
glycosyl transferase (lgtD) |
|
|
|
|
BB0576 |
Main |
hypothetical protein |
|
+ |
+ |
|
BB0598 |
Main |
UDP-N-acetylmuramate dehydrogenase |
|
+ |
+ |
|
BB0599 |
Main |
cysteinyl-tRNA synthetase |
|
|
|
|
BB0607 |
Main |
rep helicase |
|
+ |
|
|
BB0635 |
Main |
hypothetical protein |
|
+ |
|
|
BB0667 |
Main |
hypothetical protein |
|
+ |
+ |
|
BB0684 |
Main |
carotenoid biosynthesis protein |
|
+ |
|
|
BB0685 |
Main |
3-hydroxy-3-methylglutaryl-CoA reductase (mvaA) |
|
+ |
|
|
BB0699 |
Main |
ribosomal protein L19 |
|
|
|
|
BB0709 |
Main |
hypothetical protein |
|
+ |
+ |
|
BB0749 |
Main |
hypothetical protein |
|
|
|
|
BB0838 |
Main |
hypothetical protein |
|
+ |
+ |
|
BB0840 |
Main |
hypothetical protein |
+ |
+ |
+ |
|
BBA07 |
lp54 |
chpAI protein |
+ |
+ |
+ |
|
BBA24 |
lp54 |
decorin binding protein A (DbpA) |
+ |
+ |
+ |
|
BBA68|| |
lp54 |
BbCRASP-1 (17) |
+ |
+ |
+ |
|
BBA69|| |
lp54 |
hypothetical protein |
+ |
+ |
+ |
|
BBA70|| |
lp54 |
hypothetical protein |
|
|
|
|
BBB08 |
cp26 |
hypothetical protein |
|
+ |
+ |
|
BBB10 |
cp26 |
hypothetical protein |
|
|
|
|
BBB11 |
cp26 |
hypothetical protein |
|
|
|
|
BBB12 |
cp26 |
plasmid partition protein |
|
|
|
|
BBB13 |
cp26 |
hypothetical protein |
|
|
|
|
BBB14 |
cp26 |
hypothetical protein |
+ |
+ |
+ |
|
BBB19 |
cp26 |
outer surface protein C (ospC) |
+ |
+ |
+ |
|
BBB22 |
cp26 |
hypothetical protein |
|
+ |
|
|
BBB23 |
cp26 |
hypothetical protein |
|
+ |
|
|
BBC01 |
cp9 |
hypothetical protein |
|
|
|
|
BBC02|| |
cp9 |
hypothetical protein |
|
|
|
|
BBC03 |
cp9 |
hypothetical protein |
|
|
|
|
BBC06|| |
cp9 |
exported protein A (eppA) |
|
+ |
+ |
|
BBD11 |
lp17 |
hypothetical protein |
|
|
|
|
BBD15 |
lp17 |
hypothetical protein |
+ |
+ |
+ |
|
BBE16 |
lp25 |
hypothetical protein |
|
+ |
+ |
|
BBE17|| |
lp25 |
hypothetical protein |
|
+ |
+ |
|
BBE18 |
lp25 |
hypothetical protein |
|
|
|
|
BBE19 |
lp25 |
plasmid partition protein |
|
+ |
|
|
BBE20 |
lp25 |
hypothetical protein |
|
|
|
|
BBE21 |
lp25 |
hypothetical protein |
|
|
|
|
BBE22 |
lp25 |
pyrazinamidase, nicotinamidase (pncA) |
|
|
|
|
BBG06 |
lp28-2 |
hypothetical protein |
|
|
+ |
|
BBG10 |
lp28-2 |
hypothetical protein |
|
+ |
|
|
BBG17 |
lp28-2 |
hypothetical protein |
|
|
|
|
BBG18 |
lp28-2 |
hypothetical protein |
|
|
|
|
BBG19 |
lp28-2 |
hypothetical protein |
|
|
|
|
BBG22|| |
lp28-2 |
hypothetical protein |
|
|
|
|
BBG23|| |
lp28-2 |
hypothetical protein |
|
|
|
|
BBG29 |
lp28-2 |
hypothetical protein |
|
|
+ |
|
BBG31 |
lp28-2 |
hypothetical protein |
|
|
|
|
BBG32|| |
lp28-2 |
replicative DNA helicase |
|
|
|
|
BBI38|| |
lp28-4 |
hypothetical protein |
+ |
+ |
+ |
|
BBJ16 |
lp38 |
hypothetical protein |
|
|
|
|
BBJ17 |
lp38 |
plasmid partition protein |
|
|
|
|
BBJ34 |
lp38 |
hypothetical protein |
+ |
+ |
+ |
|
BBJ45 |
lp38 |
hypothetical protein |
|
|
|
*Defined as ORFs with significantly (P < 0.001) more nucleotide differences than neutral expectations. Nucleotide diversities of these ORFs are plotted in Fig. 1. Ka and Ks values are plotted in Fig. 3.
Automated function assignment.
+, Putative lipoprotein, predicted by Casjens et al. (1).§
+, Containing putative transmembrane domain, predicted using TMHMM (2).ś
+, Containing putative cleavage site in secreted proteins, predicted by using SIGNALP (3).||
ORFs selected for MLST analysis. Additional polymorphic ORFs selected as multilocus sequence typing (MLST) markers from a separate B31JD1 genome comparison: BBD14, BBJ18, BBJ19, BBQ45, BBQ48, and BBQ49.1. Casjens, S. (2000) J. Mol. Microbiol. Biotechnol. 2, 401410.
2. Sonnhammer, E. L., von Heijne, G. & Krogh, A. (1998) Proc. Int. Conf. Intell. Syst. Mol. Biol. 6, 175182.
3. Nielsen, H., Engelbrecht, J., Brunak, S. & von Heijne, G. (1997) Protein Eng. 10, 16.