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. 2013 Mar 6;41(8):4549–4564. doi: 10.1093/nar/gkt148

Table 2.

Genes uniquely required in S. Typhimurium

Ty inserts Ty reads SL inserts SL reads SL ID SL gene length Ty ID Ty gene length Name Function
No orthologue in S. Typhi
18 123 SL0742 1269 putative cation transporter
9 80 SL0830 516 conserved hypothetical protein
4 21 SL0831 855 putative electron transfer flavoprotein (beta subunit)
0 0 SL0950 323 predicted bacteriophage protein, potential phage repressor Gifsy-2
11 75 SL1179 789 envF lipoprotein
3 18 SL1480 249 antitoxin Phd_YefM, type II toxin-antitoxin system
4 32 SL1527 264 ydcX putative inner membrane protein
1 3 SL1560 717 putative membrane protein
7 50 SL1601 859 putative transcriptional regulator (pseudogene)
4 36 SL1799 201 bacteriophage encoded pagK (phoPQ-activated protein)
5 22 SL1830A 434 conserved hypothetical protein (pseudogene)
3 27 SL1967 677 predicted bacteriophage protein, potential phage repressor SLP203
1 15 SL2045A 63 yoeI short ORF
17 107 SL2066 900 rfbJ CDP-abequose synthase
3 34 SL2549 209 endodeoxyribonuclease
4 149 SL2593 449 putative DNA-binding protein, potential phage repressor Gifsy-1 SLP272
3 7 SL2633 846 putative repressor protein, phage SLP281
21 SL2695 978 smf putative competence protein
5 39 SL4132 291 hypothetical protein
5 45 SL4354A 303 conserved hypothetical protein
Present in S. Typhi but required only in S. Typhimurium*
    36 474 5 26 SL0032 441 t0033 306 putative transcriptional regulator
    71 349 11 48 SL0623 642 t2232 576 lipB lipoate-protein ligase B
    151 3546 10 64 SL0702 897 t2156 894 putative glycosyl transferase
    194 3007 9 61 SL0703 1134 t2155 1134 galactosyltransferase
    231 3499 15 67 SL0706 1779 t2152 1780 putative glycosyltransferase, cell wall biogenesis
    84 1041 2 4 SL0707 834 t2151 834 putative glycosyltransferase, cell wall biogenesis
    49 367 14 70 SL0722 1569 t2136 1569 cydA cytochrome d ubiquinol oxidase subunit I
    74 1613 5 22 SL1069 693 t1789 693 putative secreted protein
    20 199 1 1 SL1203 150 t1146 156 hypothetical protein
    20 290 1 5 SL1264 315 t1209 315 putative membrane protein
    84 384 6 26 SL1327 402 t1261 384 spiC putative pathogenicity island 2 secreted effector protein
    66 769 5 35 SL1331 270 t1265 327 sseA T3SS chaperone
    36 307 2 5 SL1341 228 t1275 228 ssaH putative pathogenicity island protein
    47 407 1 3 SL1342 249 t1276 249 ssaI putative pathogenicity island protein
    144 3197 5 14 SL1343 750 t1277 750 ssaJ putative pathogenicity island lipoprotein
    63 847 5 26 SL1354 267 t1288 267 ssaS putative type III secretion protein
    73 762 4 44 SL1355 780 t1289 780 ssaT putative type III secretion protein
    30 226 12 48 SL1386 693 t1322 693 rnfE/ydgQ Electron transport complex protein rnfE
    265 3337 29 165 SL1473 1557 t1463 1557 pqaA PhoPQ-activated protein
    85 765 6 35 SL1532 951 t1511 951 sifB putative virulence effector protein
    22 156 16 174 SL1561 1227 t1534a 141 sseJ Salmonella translocated effector protein (SseJ)
    119 1639 10 44 SL1563 762 t1536 762 putative periplasmic amino acid-binding protein
    107 2440 5 44 SL1564 648 t1537 648 putative ABC amino acid transporter permease
    183 1646 20 118 SL1628 1355 t1612 1364 hypothetical protein
    23 177 1 5 SL1659 183 t1640 183 yciG conserved hypothetical protein
    78 617 16 104 SL1684 1014 t1664 1014 Hnr putative regulatory protein
    37 277 4 25 SL1785 396 t1022 396 conserved hypothetical protein
    166 2823 9 27 SL1793 915 t1016 915 pagO inner membrane protein
    28 311 3 22 SL1794 159 t1015 159 putative inner membrane protein
    23 155 1 4 SL1823 972 t0988 972 msbB lipid A acyltransferase
    60 402 11 58 SL2064 1002 t0786 1002 rfbV putative glycosyl transferase
    87 524 7 59 SL2065 1293 t0785 1299 rfbX putative O-antigen transporter
    66 559 13 74 SL2069 774 t0780 774 rfbF glucose-1-phosphate cytidylyltransferase
    41 204 5 14 SL3828 1830 t3658 1830 glmS glucosamine-fructose-6-phosphate aminotransferase
    27 288 5 23 SL4250 288 t4220 288 putative GerE family regulatory protein
    148 2633 16 89 SL4251 876 t4221 876 araC family regulatory protein

Genes determined to be uniquely required in S. Typhimurium. SL, S. Typhimurium; Ty, S. Typhi; inserts refer to the number of unique insertion sites within a gene; reads refer to the number of sequence reads over all insertions sites within a gene. Shaded rows indicate genes shown to be H-NS repressed in (61).

*P-value (associated with log2 read ratio) < 0.05.

asseJ is a pseudogene in S. Typhi.