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Table 2
Characteristics of the ORFs located in the E. coli O102 O-antigen gene cluster
Gene
name
Position of
gene
G+C
content
(%)
Conserved domain(s)
Similar protein(s), strain(s)
(Genbank accession No.)
%Identical aa /%similar aa
(total No. of aa)
Putative function of
protein
rmlB
rmlD
rmlA
rmlC
wzx
707..1792
42.3
46.1
44.0
35.2
33.1
NAD dependent epimerase/
dehydratase family (PF01370)
E value = 1.5 Â eÀ215
dTDP-glucose 4,6-
dehydratase
Shigella flexneri 2a str. 301
(AAN43643)
94/96(361)
86/90(300)
96/98(292)
78/85(182)
49/69(384)
dTDP-glucose 4,6-
dehydratase
1792..2694
2752..3630
3635..4183
4252..5439
RmlD substrate binding domain
(PF04321)
dTDP-6-deoxy-
dehydrogenase
L-mannose
dTDP-6-deoxy-
dehydrogenase
L-mannose
E value = 2.8 Â eÀ74
Shigella flexneri 2a str. 301
(AAN43642)
Glucose-1-phosphate
thymidylyl transferase
Shigella flexneri 2a str. 301
(AAN43641)
dTDP-4-dehydrorhamnose
3,5-epimerase
Shigella flexneri 2a str. 301
(AAN43640)
Nucleotidyl transferase (PF00483)
Glucose-1-phosphate
thymidylyl transferase
E value = 3.2 Â eÀ115
dTDP-4-dehydrorhamnose 3,5-
epimerase
dTDP-4-
dehydrorhamnose 3,5-
epimerase
(PF00908)
E value = 6.8 Â eÀ114
Polysaccharide biosynthesis protein
(PF01943)
Putative O-antigen
transporter
Shigella flexneri 2a str. 301
(AAN43639)
Putative O-antigen
transporter
E value = 7.6 Â eÀ32
welL
wzy
5433..6461
6442..7572
7569..8501
8498..9550
9554..10291
27.2
28.3
31.2
29.6
29.5
Eps9K
34/59(194)
25/47(359)
35/56(272)
34/53(355)
46/67(248)
Glycosyl transferase
O-Antigen polymerase
Glycosyl transferase
Glycosyl transferase
Galactosyl transferase
Streptococcus thermophilus
(AAN63754)
Putative polymerase
Bacteroides fragilis
(AAG26475)
Glycosyl transferase
Clostridium acetobutylicum
(AAK80132)
wbcM
Yersinia enterocolitica
(CAA87701)
Glycosyl transferase
Escherichia coli O157:H7
EDL933
O-antigen Polymerase (PF04932)
E value = 9.0 Â eÀ2
welM
welN
welO
Glycos_transf_2 (PF00535)
E value = 8.1 Â eÀ44
Glycos_transf_1 (PF00534)
E value = 2.1 Â eÀ36
Glycos_transf_2 (PF00535)
E value = 7.0 Â eÀ37
(AAG57100)
gne
10330..11349 34.0
NAD dependent epimerase/
dehydratase family (PF01370)
E value = 2.8 Â e-74
Gne
58/75(336)
UDP-N-
acetylglucosamine-4-
epimerase
Yersinia enterocolitica
(AAC60777)
resonance (NMR) spectra were recorded on a Bruker Avance II 600
spectrometer (Germany) at 30 °C using internal TSP (dH 0) and ace-
tone (dC 31.45) as reference. 2D NMR spectra were obtained using
standard Bruker software, and Bruker TopSpin2.1 program was used
to acquire and process the NMR data. A mixing time of 100 and
150 ms was used in TOCSY and ROESY experiments, respectively.
Targeted Program for Research and Development in Priority Areas
of Russia’s Science and Technology Complex for 2007–2013 (State
Contract No. 16.552.11.7050), the National Natural Science Foun-
dation of China (30900255 and 31111120026), and Tianjin Re-
search Program of Application Foundation and Advanced
Technology (10JCYBJC10100).
1.5. Sequencing and analysis of genes
References
Chromosomal DNA was prepared as described previously.20 The
primers (#1523 and #1524) based on the housekeeping genes galF
and gnd,21 respectively, were used to amplify the O-antigen gene
clusters of the E. coli strains. The PCR cycles used were as follows:
denaturation at 94 °C for 10 s, annealing at 60 °C for 30 s, and
extension at 68 °C for 15 min. Shotgun banks were constructed
for each strain as described previously.22 Sequencing was carried
out using an ABI 3730 automated DNA sequencer (Applied Biosys-
tems, Foster City, CA), and sequence data were analyzed using
computer programs as described previously.23 The DNA sequence
of O-antigen gene clusters of E. coli O102 has been deposited in
GenBank under the accession numbers JX087966.
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Acknowledgements
This work was supported by the Russian Foundation for Basic
Research (projects 11-04-91173-a and 11-04-01020-a), the Federal