Salmonella Enteritidis gene with SNP | Type of SNP as referenced to S. Enteritidis PT4 | Location of SNP in S. Enteritidis PT4 genome | Salmonella Enteritidisa | Other Salmonella enterica subsp. I serotypesb,c | Outlier microbes | ||||||||||||||||||||
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 |  |  |  |  |  | O-antigen serotype |  |  |  | ||||||||||||||||
 |  |  | D1 | D1 | D1 | D1 | D1 | D1 | D1 | A | D1 | B | B | B | B | B | B | C1 | C1 | C2 | C2 | C3 | na | na | na |
 |  |  | PT 13a 21046 | PT13a 21027 | PT4 22079 (same as reference) | Gallinarum | Dublin | Typhi | Paratyphi A | Javiana | Typhimurium LT2 | Typhimurium DT104 | Typhimurium 4,[5],12:i:- | Saintpaul | Schwarzengrund | Heidelberg | Agona | Choleraesuis | Infantis | Hadar | Newport | Kentucky | Salmonella enterica subsp. arizonae | Salmonella bongori | E. coli 0157:H7 Sakai |
A) Polymorphisms that distinguish PT13a 21046 from PT13a 21027 and S. Enteritidis PT4 | |||||||||||||||||||||||||
fhuA (SEN0196) | substitution: ORF termination | 226922 | - | + | + | + (78) | + (78) | - (23) | - (23) | + (78) | + (78) | + (78) | + (78) | + (78) | + (78) | + (99) | + (100) | + (78) | + (78) | + (78) | + (78) | + (99) | + (97) | + (99) | + (93) |
mocR (SEN3898) | deletion: 92 bp | 4189388-4189479 | - | + | + | + (100) | + (99) | + (98) | + (98) | nd | - nd | - nd | - nd | - nd | - nd | - nd | - nd | - nd | - nd | - nd | - nd | - nd | - nd | - nd | - nd |
DGC (SEN4316) | deletion: 80 bp of 5' end + 135 bp upstream | 4642252-4642331 | - | + | + | + (99) | + (99) | + (99) | + (99) | + (99) | + (99) | + (99) | + (99) | + (99) | + (99) | + (99) | + (99) | + (99) | + (99) | + (99) | + (99) | + (99) | + (90) | + (90) | - nd |
B) Polymorphisms that distinguish PT13a 21027 from PT13a 21046 and S. Enteritidis PT4 | |||||||||||||||||||||||||
foxA (SEN0347) | deletion: 1 bp | 393529 | + | - | + | - (99) | + (99) | + (98) | + (99) | + (99) | + (99) | + (99) | + (99) | + (99) | + (99) | + (99) | + (99) | + (99) | + (99) | + (98) | + (99) | + (99) | - nd | - nd | - nd |
putP (SEN0989) | substitution: ORF termination | 1095448 | + | - | + | + (99) | + (100) | - nd | + (100) | + (100) | + (99) | + (99) | + (99) | + (99) | + (99) | + (100) | - nd | - (44) | + (100) | + (99) | + (100) | - (nd) | + (99) | - nd | - nd |
kdgM (SEN0992) | deletion: 1 bp | 1099079 | + | - | + | + (99) | + (99) | + (97) | + (99) | + (98) | + (99) | + (99) | + (99) | + (99) | + (98) | + (99) | - nd | + (99) | + (99) | + (99) | + (99) | - nd | + (96) | - nd | - nd |
ydcZ (SEN1464) | deletion: 6 bp | 1554930 | + | - | + | + (100) | + (99) | + (99) | + (98) | + (99) | + (99) | + (99) | + (99) | + (100) | + (100) | + (98) | + (99) | + (99) | + (98) | + (99) | + (99) | + (99) | + (95) | - nd | - nd |
ydjN (SEN1723) | substitution: ORF termination | 1828544 | + | - | + | + (99) | + (99) | + (99) | + (99) | + (99) | + (100) | + (100) | + (100) | + (100) | + (99) | + (100) | + (99) | + (99) | + (100) | + (100) | + (99) | + (100) | + (99) | + (99) | + (96) |
ytcJ-like (SEN1576) | substitution: ORF termination | 1681327 | + | - | + | + (99) | + (99) | + (99) | + (98) | + (98) | + (99) | + (99) | na | + (98) | + (98) | + (99) | + (99) | + (98) | + (99) | + (99) | + (99) | + (99) | - nd | + (96) | - nd |
pgk (SEN2751) | deletion: 12 bp in-frame | 2939833-2939844 | + | - | + | + (99) | + (97) | + (98) | + (97) | + (99) | + (98) | + (98) | + (98) | + (98) | + (99) | + (98) | + (97) | - (80) | + (97) | + (98) | + (98) | + (97) | + (99) | + (85) | - nd |
cysN (SEN2773) | substitution: ORF termination | 2957802 | + | - | + | + (99) | + (99) | + (99) | + (99) | + (99) | + (99) | + (99) | + (99) | + (99) | + (99) | + (99) | + (99) | + (99) | + (99) | + (99) | + (99) | + (99) | + (99) | + (92) | + (87) |
dsdA (SEN3619) | deletion: 10 bp | 3880104-3880113 | + | - | + | + (100) | + (99) | + (99) | + (99) | + (99) | + (99) | + (99) | + (99) | + (99) | + (99) | + (100) | + (99) | + (99) | + (99) | + (99) | + (100) | + (99) | + (97) | - nd | - nd |
lrgB (SEN4042) | deletion: 12 bp in-frame | 4368126-4368137 | + | - | + | + (100) | + (99) | + (99) | + | + (100) | + (100) | + (100) | + (100) | + (100) | + (100) | + (100) | + (100) | + (100) | + (100) | + (100) | + (100) | + (100) | + (99) | + (97) | - nd |
yjfK (SEN4139) | shared deletion: fusion of yjfK and yjfL; ribosomal binding site of yjfL removed | 4472579-4472589 | + | - | + | + (99) | + (99) | + (99) | + (99) | + (99) | + (99) | + (100) | + (100) | + (100) | + (99) | + (100) | + (99) | + (99) | + (100) | + (100) | + (100) | + (99) | - nd | - (89) | - nd |
yjfL (SEN4140) | Â | Â | + | - | + | - nd | + (100) | + (99) | + (100) | + (99) | + (100) | + (100) | + (99) | + (100) | + (99) | + (100) | + (99) | + (99) | + (100) | + (100) | + (100) | + (99) | - (nd) | + (98) | - (nd) |
sefD (SEN4250) | deletion: single bp | 4574262 | + | - | + | - (99) | + (100) | - (99) | - (99) | - nd | - nd | - nd | - nd | - nd | - nd | - nd | - nd | - nd | - nd | - nd | - nd | - nd | - nd | - nd | - nd |
a Abbreviations and symbols: na, possible error in contig assembly or database or otherwise not applicable; nd, no similar gene detected; nucleotide sequence similarity rather than amino acid sequence similarity is included for genes that are pseudogenes, which are recorded by a "-" even if percent nucleotide similarity is high. | |||||||||||||||||||||||||
b Numbers in parentheses indicate % similarty between translated amino acid sequences of S. Enteritidis in comparison to indicated serotype, unless a pseudogene is present and reported as nucleotide similarity. | |||||||||||||||||||||||||
c Strains and databases referenced are: | |||||||||||||||||||||||||
Serotype designation | Refseq: | Genbank accession | Â | Â | Â | Â | Â | Â | Â | Â | Â | Â | Â | Â | Â | Â | Â | Â | Â | Â | |||||
Salmonella enterica subsp. arizonae serovar 62:z4,z23:--, complete genome | NC_010067 | CP000880 | Â | Â | Â | Â | Â | Â | Â | Â | Â | Â | Â | Â | Â | Â | Â | Â | Â | Â | |||||
Salmonella enterica subsp. enterica serovar 4,[5],12:i:- str. CVM23701 | NZ_ABAO00000000 | ABAO00000000 | Â | Â | Â | Â | Â | Â | Â | Â | Â | Â | Â | Â | Â | Â | Â | Â | Â | Â | |||||
Salmonella enterica subsp. enterica serovar Agona str. SL483 | NZ_ABEK00000000 | ABEK00000000 | Â | Â | Â | Â | Â | Â | Â | Â | Â | Â | Â | Â | Â | Â | Â | Â | Â | Â | |||||
Salmonella enterica subsp. enterica serovar Choleraesuis str. SC-B67 | NC_006905 | AE017220 | Â | Â | Â | Â | Â | Â | Â | Â | Â | Â | Â | Â | Â | Â | Â | Â | Â | Â | |||||
Salmonella enterica subsp. enterica serovar Dublin str. CT_02021853 | NZ_ABAP00000000 | ABAP00000000 | Â | Â | Â | Â | Â | Â | Â | Â | Â | Â | Â | Â | Â | Â | Â | Â | Â | Â | |||||
Salmonella enterica subsp. enterica serovar Heidelberg str. SL476 | NC_011083 | CP001120 | Â | Â | Â | Â | Â | Â | Â | Â | Â | Â | Â | Â | Â | Â | Â | Â | Â | Â | |||||
Salmonella enterica subsp. enterica serovar Heidelberg str. SL486 | NZ_ABEL00000000 | ABEL00000000 | Â | Â | Â | Â | Â | Â | Â | Â | Â | Â | Â | Â | Â | Â | Â | Â | Â | Â | |||||
Salmonella enterica subsp. enterica serovar Javiana str. GA_MM04042433 | NZ_ABEH00000000 | ABEH00000000 | Â | Â | Â | Â | Â | Â | Â | Â | Â | Â | Â | Â | Â | Â | Â | Â | Â | Â | |||||
Salmonella enterica subsp. enterica serovar Kentucky str. CDC 191 | NZ_ABEI00000000 | ABEI00000000 | Â | Â | Â | Â | Â | Â | Â | Â | Â | Â | Â | Â | Â | Â | Â | Â | Â | Â | |||||
Salmonella enterica subsp. enterica serovar Kentucky str. CVM29188 | NZ_ABAK00000000 | ABAK00000000 | Â | Â | Â | Â | Â | Â | Â | Â | Â | Â | Â | Â | Â | Â | Â | Â | Â | Â | |||||
Salmonella enterica subsp. enterica serovar Newport str. SL254 | NC_011080 | CP000604 | Â | Â | Â | Â | Â | Â | Â | Â | Â | Â | Â | Â | Â | Â | Â | Â | Â | Â | |||||
Salmonella enterica subsp. enterica serovar Newport str. SL317 | NZ_ABEW00000000 | ABEW00000000 | Â | Â | Â | Â | Â | Â | Â | Â | Â | Â | Â | Â | Â | Â | Â | Â | Â | Â | |||||
Salmonella enterica subsp. enterica serovar Paratyphi A str. ATCC 9150 | NC_006511 | CP000026 | Â | Â | Â | Â | Â | Â | Â | Â | Â | Â | Â | Â | Â | Â | Â | Â | Â | Â | |||||
Salmonella enterica subsp. enterica serovar Saintpaul str. SARA23 | NZ_ABAM00000000 | ABAM00000000 | Â | Â | Â | Â | Â | Â | Â | Â | Â | Â | Â | Â | Â | Â | Â | Â | Â | Â | |||||
Salmonella enterica subsp. enterica serovar Saintpaul str. SARA29 | NZ_ABAN00000000 | ABAN00000000 | Â | Â | Â | Â | Â | Â | Â | Â | Â | Â | Â | Â | Â | Â | Â | Â | Â | Â | |||||
Salmonella enterica subsp. enterica serovar Schwarzengrund str. CVM19633 | NC_011094 | CP001127 | Â | Â | Â | Â | Â | Â | Â | Â | Â | Â | Â | Â | Â | Â | Â | Â | Â | Â | |||||
Salmonella enterica subsp. enterica serovar Schwarzengrund str. SL480 | NZ_ABEJ00000000 | ABEJ00000000 | Â | Â | Â | Â | Â | Â | Â | Â | Â | Â | Â | Â | Â | Â | Â | Â | Â | Â | |||||
Salmonella enterica subsp. enterica serovar Typhi Ty2 | NC_004631 | AE014613 | Â | Â | Â | Â | Â | Â | Â | Â | Â | Â | Â | Â | Â | Â | Â | Â | Â | Â | |||||
Salmonella enterica subsp. enterica serovar Typhi str. CT18 | NC_003198 | AL513382 | Â | Â | Â | Â | Â | Â | Â | Â | Â | Â | Â | Â | Â | Â | Â | Â | Â | Â | |||||
Salmonella typhimurium LT2 | NC_003197 | AE006468 | Â | Â | Â | Â | Â | Â | Â | Â | Â | Â | Â | Â | Â | Â | Â | Â | Â | Â | |||||
E. coli 0157:H7 Sakai | NC_002695 | BA000007 | Â | Â | Â | Â | Â | Â | Â | Â | Â | Â | Â | Â | Â | Â | Â | Â | Â | Â | |||||
Sanger Institute databases are available at http://www.sanger.ac.uk/Projects/Salmonella/. | |||||||||||||||||||||||||
Salmonella bongori 12419 ATCC 43975 | |||||||||||||||||||||||||
Salmonella enterica Enteritidis PT4 NCTC 13349 | |||||||||||||||||||||||||
Salmonella enterica Gallinarum 287/91 NCTC 13346 |