Figure 1Alignment of SHI-O loci of strains NCCP 15744, 2457T, Sf301, and 2002017.
Table 1Average of nucleotide identities (ANI) of strain NCCP 15744 compared to 3 reference strains (2002017, Sf301, and 2457T)
Target |
Query |
ANIb |
ANIb alignments |
ANIb aligned |
2002017 |
NCCP 15744 |
99.91% |
4,557 (95.49%) |
4,642,181 (95.36%) |
Sf301 |
NCCP 15744 |
99.83% |
4,446 (93.17%) |
4,519,560 (92.83%) |
2457T |
NCCP 15744 |
99.84% |
2,264 (93.55%) |
4,540,984 (93.20%) |
Table 2Genome features of Shigella flexneri NCCP 15744 and 2002017
|
Features of NCCP 15744 |
Features of 2002017 |
|
|
Chromosome |
Plasmids |
Chromosome |
Plasmids |
|
|
pSFII_1 |
pSFII_2 |
pSFII_3 |
pSFII_4 |
pSFXV_1 |
pSFXV_2 |
pSFXV_3 |
pSFXV_4 |
pSFXV_5 |
Total length (bp) |
4,631,995 |
223.049 |
6,200 |
4,042 |
3,117 |
4,650,865 |
223.364 |
6,850 |
6,200 |
4,042 |
3,180 |
|
No. of ORFs |
4,268 |
293 |
8 |
4 |
5 |
4,372 |
302 |
11 |
8 |
4 |
6 |
|
Percentage of CDS (%) |
79.6 |
75.2 |
71.47 |
58.86 |
27.43 |
83.3 |
79.3 |
64.2 |
71.5 |
58.9 |
61.8 |
|
G+C content (%) |
50.86 |
45.92 |
45.92 |
52.55 |
45.4 |
50.86 |
45.92 |
|
45.92 |
52.55 |
45.4 |
|
IS elements (%) |
336 (7) |
|
|
|
|
491 (6) |
157 (32) |
1 |
0 |
0 |
0 |
|
No. of pseudogenes |
216 |
|
|
|
|
232 |
|
|
|
|
|
|
No. of rRNAs |
13 |
13 |
|
|
|
22 |
|
|
|
|
|
|
No. of tRNAs |
98 |
98 |
|
|
|
101 |
|
|
|
|
|
Table 3The list of genes lost in strain NCCP 15744 compared to strain 2002017 in the SHI-O genomic island
No. |
Locus_tag |
Gene product |
Function |
1 |
SFXV_0311 |
Hypothetical protein |
Unknown |
2 |
SFXV_0312 |
Putative bacteriophage protein |
|
3 |
SFXV_0313 |
Hypothetical protein |
|
4 |
SFXV_0315 |
Hypothetical protein |
|
5 |
SFXV_0316 |
Hypothetical protein |
|
6 |
SFXV_0317 |
Putative phage-related DNA recombination protein |
|
7 |
SFXV_0318 |
Hypothetical protein |
|
8 |
SFXV_0322 |
Antitermination of transcription at nut site protein |
Immunity and regulation |
9 |
SFXV_0323 |
CI protein |
|
10 |
SFXV_0323a |
cro protein |
|
11 |
SFXV_0324 |
Putative regulatory protein CII of bacteriophage |
|
12 |
SFXV_0327a |
Gp56 |
DNA replication and recombination |
13 |
SFXV_0327b |
Gp60 |
|
14 |
SFXV_0328a |
NinD protein |
|
15 |
SFXV_0328b |
NinE protein |
|
16 |
SFXV_0335 |
Rz protein |
Lysis |
17 |
SFXV_0335a |
Hypothetical protein |
|
18 |
SFXV_0335b |
Hypothetical protein |
|
19 |
SFXV_0347 |
Gene 10 protein |
DNA packaging & head and tail morphogenesis |