Table 2 |
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|
Regions larger than 5 kb showing some of the characteristics1 of bacteriophages (ϕ) and GIs. |
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|
Type |
Size (kb) |
GC content |
CDSs |
Description relevant content |
|
|
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|
Chr I |
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|
ϕ VS1 |
8.8 |
33.9 |
VSAL_I0388-I0398 |
Putative remnant harbouring shufflon-specific DNA recombinase |
|
ϕ VS2 |
15.2 |
40.5 |
VSAL_I0764-I0783 |
Compound transposon harbouring phage remnants |
|
ϕ VS3 |
6.8 |
34.3 |
VSAL_I0966-I0969 |
Putative phage remnant harbouring a phage integrase |
|
ϕ VS4 |
34.1 |
40.8 |
VSAL_I1008-I1051 |
Complete K139-like phage. Flanked by one IS element |
|
ϕ VS5 |
10.7 |
31.5 |
VSAL_I1921-I1930 |
Phage remnant harbouring putative exported proteins. Flanked by one IS element |
|
ϕ VS6 |
12.2 |
36.2 |
VSAL_I2480-I2489 |
Putative phage remnant harbouring a phage integrase. Flanked by one IS element |
|
GI-VS1 |
18.9 |
36.7 |
VSAL_I0019-I0035 |
Compound transposon harbouring duplicated plasmid genes |
|
GI-VS2 |
13.7 |
38.3 |
VSAL_I0056-I0070 |
Compound transposon encoding chromosome partitioning proteins |
|
GI-VS3 |
18.8 |
39.8 |
VSAL_I0129-I0144 |
Compound transposon encoding proteins involved in siderophore synthesis and uptake |
|
GI-VS4 |
13.9 |
40.6 |
VSAL_I0884-I0872 |
Putative GI, encoding exported proteins, a peptidase and a nuclease |
|
GI-VS5 |
24.2 |
38.2 |
VSAL_I1105-I1125 |
Putative GI encoding a putative protein secretion system (T6SSI). Flanked by one IS element |
|
GI-VS6 |
23.5 |
36.8 |
VSAL_I1166-I1185 |
Compound transposon encoding a putative protein secretion system (T6SSII) |
|
GI-VS7 |
19.7 |
35.9 |
VSAL_I1463-I1492 |
Compound transposon encoding a antibiotic resistance protein and a cold-shock protein |
|
GI-VS8 |
10.5 |
33.3 |
VSAL_I1620-I1633 |
Compound transposon encoding various proteins with unknown function |
|
GI-VS9 |
10.9 |
39.9 |
VSAL_I1787-I1794 |
Putative GI, encoding a restriction enzyme and a DNA methylase |
|
GI-VS10 |
38.2 |
36.2 |
VSAL_I3009-I3042 |
Compound transposon encoding proteins involved in LPS and CPS biosynthesis |
|
Chr II |
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|
ϕ VSA1 |
26.4 |
36.4 |
VSAL_II0534-II0566 |
Putative phage remnant harbouring a toxin and an antitoxin |
|
ϕ VSA2 |
6.5 |
34.6 |
VSAL_II0629-II0638 |
Putative phage remnant harbouring a phage integrase |
|
ϕ VSA3 |
5.1 |
35.7 |
VSAL_II0739-II0745 |
Putative remnant harbouring genes for phage replication |
|
GI-VSA1 |
13.7 |
39.1 |
VSAL_II0117-II0128 |
Compound transposon encoding an ABC transporter. Flanked by one IS element |
|
GI-VSA2 |
6.4 |
34.6 |
VSAL_II0202-II0208 |
Compound transposon encoding an acyltransferase and hypothetical proteins |
|
GI-VSA3 |
16.2 |
38.2 |
VSAL_II0257-II0272 |
Compound transposon encoding exported and membrane proteins |
|
GI-VSA4 |
15.8 |
37.9 |
VSAL_II0321-II0335 |
Putative GI encoding a glycosyl transferase and membrane proteins. Flanked by one IS element |
|
GI-VSA5 |
15.4 |
35.3 |
VSAL_II0362-II0380 |
Putative GI encoding a protein secretion system (Flp-type pilus) |
|
GI-VSA6 |
8.9 |
37.9 |
VSAL_II0986-II0990 |
Putative GI encoding hypothetical proteins. Flanked by IS element |
|
|
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|
The genome position, sizes, number of CDSs and G+C content of the phages and GIs are listed, together with a description of the most important content2. 1Abnormal G+C content; GC deviation; repeats flanking the ends; insertion next tRNAs; and the presence of phage genes. 2A complete list of the CDSs are provided in [Additional file 10]. |
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|
Hjerde et al. BMC Genomics 2008 9:616 doi:10.1186/1471-2164-9-616 |
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