TABLE 2.
Sources of sequences included in the reference sequence database for Shigella serotypinga
| Sequence | Source | Accession no. | Gene identifier(s) | Beginning position | Ending position | Complement | Length (bp) | Reference(s) |
|---|---|---|---|---|---|---|---|---|
| ipaH_C | S. flexneri 2a 301 chromosome | AE005674.2 | ipaH_7 | 2686919 | 2687698 | 780 | 91 | |
| ipaB | S. sonnei pSS_046 | CP000039.1 | ipaB | 84468 | 86210 | x | 1,743 | 92 |
| Ss_methylase | S. sonnei SS046 chromosome | CP000038.1 | SSON_1583 | 1663456 | 1665288 | 1,833 | 55 | |
| Ss_wzx | S. sonnei pSS_046 | CP000039.1 | wzx | 197086 | 198354 | 1,269 | 13, 92 | |
| Ss_wzy | S. sonnei pSS_046 | CP000039.1 | wzy | 198423 | 199595 | 1,173 | 13, 92 | |
| Sf_wzx | S. flexneri 2a 301 chromosome | AE005674.2 | rfbE | 2113945 | 2115201 | x | 1,257 | 36, 91 |
| Sf_wzy | S. flexneri 2a 301 chromosome | AE005674.2 | rfc | 2110959 | 2112107 | x | 1,149 | 36, 91 |
| Sf6_wzx | S. flexneri 6 NCTC9779 O-Ag cluster | EU118169 | wzx | 4509 | 5741 | 1,233 | 10 | |
| Sf6_wzy | S. flexneri 6 NCTC9779 O-Ag cluster | EU118169 | wzy | 5797 | 6984 | 1,188 | 10 | |
| GtrI | S. flexneri 1a 0439 chromosome | CP020342.1 | BS647_00210 | 24836 | 25787 | x | 952 | 39, 42 |
| GtrII | S. flexneri 2a 301 chromosome | AE005674.2 | gtrII | 319152 | 320612 | 1,461 | 91 | |
| GtrIV | Shigella phage SfIV | NC_022749 | V416_gp25 | 20408 | 21721 | x | 1,314 | 93 |
| GtrV | S. flexneri 5 8401 chromosome | CP000266 | gtrV | 274667 | 275920 | x | 1,254 | 40, 94 |
| GtrX | S. flexneri 4c 1205 chromosome | CP012140 | AD871_01870 | 346525 | 347790 | x | 1,266 | 95 |
| GtrIC | S. flexneri 7b 3007 | CP024473 | Unannotated | 4289665 | 4291260 | 1,596 | 96 | |
| Oac | Enterobacterial phage Sf6 | AF547987 | 15 | 15624 | 16625 | x | 1,002 | 37, 97 |
| Oac1b | Partial sequence from S. flexneri 1b | JF450728.1 | oac | 2673 | 3674 | 1,002 | 53 | |
| Xv | pSFxv_2 from strain 2002017 | NC_017320.1 | SFXV_RS26800 | 1523 | 3043 | x | 1,521 | 15, 98 |
| Sd1_wzx | S. dysenteriae 1 Sd197 chromosome | CP000034 | rfbX | 2010259 | 2011449 | 1,191 | 14, 99 | |
| Sd1_wzy | S. dysenteriae 1 Sd197 chromosome | CP000034 | rfc | 2011446 | 2012588 | 1,143 | 14, 99 | |
| Sd1_rfp | S. dysenteriae 1 pSD197_spA | CP000640 | rfpB | 2979 | 4112 | x | 1,134 | 14, 38, 99 |
| Sd2_wzx | S. dysenteriae 2 O-Ag cluster | EU296404 | wzx | 5775 | 7202 | 1,428 | 10 | |
| Sd2_wzy | S. dysenteriae 2 O-Ag cluster | EU296404 | wzy | 1867 | 2952 | 1,086 | 10 | |
| Sd3_wzx | S. dysenteriae 3 O-Ag cluster | EU296415 | wzx | 1111 | 2625 | 1,515 | 10 | |
| Sd3_wzy | S. dysenteriae 3 O-Ag cluster | EU296415 | wzy | 7014 | 8117 | 1,104 | 10 | |
| Sd4_wzx | S. dysenteriae 4 O-Ag cluster | EU296402 | wzx | 1081 | 2352 | 1,272 | 10 | |
| Sd4_wzy | S. dysenteriae 4 O-Ag cluster | EU296402 | wzy | 4769 | 6001 | 1,233 | 10 | |
| Sd5_wzx | S. dysenteriae 5 O-Ag cluster | EU294174 | wzx | 4728 | 5915 | 1,188 | 10 | |
| Sd5_wzy | S. dysenteriae 5 O-Ag cluster | EU294174 | wzy | 9803 | 11134 | 1,332 | 10 | |
| Sd6_wzx | S. dysenteriae 6 O-Ag gene cluster | EU296414 | wzx | 340 | 1614 | 1,275 | 10 | |
| Sd6_wzy | S. dysenteriae 6 O-Ag gene cluster | EU296414 | wffH_5 (including the fusion junction between wzy and wffH) | 3592 | 4722 | 1,131 | 10 | |
| Sd7_wzx | S. dysenteriae 7 O-Ag gene cluster, strain M1354 | AY380835 | wzx | 7707 | 9194 | 1,488 | 45 | |
| Sd7_wzy | S. dysenteriae 7 O-Ag gene cluster, strain M1354 | AY380835 | wzy | 10646 | 11836 | 1,191 | 45 | |
| Sd8_wzx | S. dysenteriae 8 O-Ag gene cluster | EU294166 | wzx | 3180 | 4349 | 1,170 | 10 | |
| Sd8_wzy | S. dysenteriae 8 O-Ag gene cluster | EU294166 | wzy | 1899 | 3125 | 1,227 | 10 | |
| Sd9_wzx | S. dysenteriae 9 O-Ag gene cluster | EU296416 | wzx | 7775 | 9055 | 1,281 | 10 | |
| Sd9_wzy | S. dysenteriae 9 O-Ag gene cluster | EU296416 | wzy | 5373 | 6578 | 1,206 | 10 | |
| Sd10_wzx | S. dysenteriae 10 O-Ag gene cluster | EU294178 | wzx | 4706 | 5866 | 1,161 | 10 | |
| Sd10_wzy | S. dysenteriae 10 O-Ag gene cluster | EU294178 | wzy | 6933 | 8354 | 1,422 | 10 | |
| Sd11_wzx | S. dysenteriae 11 O-Ag gene cluster | EU294172 | wzx | 3741 | 5141 | 1,401 | 10 | |
| Sd11_wzy | S. dysenteriae 11 O-Ag gene cluster | EU294172 | wzy | 5138 | 6301 | 1,164 | 10 | |
| Sd12_wzx | S. dysenteriae 12 O-Ag gene cluster | EU294169 | wzx | 5663 | 6874 | 1,212 | 10 | |
| Sd12_wzy | S. dysenteriae 12 O-Ag gene cluster | EU294169 | wzy | 7882 | 8955 | 1,074 | 10 | |
| Sd13_wzx | S. dysenteriae 13 O-Ag cluster | EU294167 | wzx | 5631 | 7133 | 1,503 | 10 | |
| Sd13_wzy | S. dysenteriae 13 O-Ag cluster | EU294167 | wzy | 11011 | 12108 | 1,098 | 10 | |
| Sd14_wzx | S. dysenteriae 14 ATCC 49346 chromosome | CP026832 | Unannotated | 2829534 | 2830799 | x | 1,266 | 54, this study |
| Sd14_wzy | S. dysenteriae 14 ATCC 49346 chromosome | CP026832 | Unannotated | 2831775 | 2832977 | x | 1,203 | 54, this study |
| Sd15_wzx | S. dysenteriae 15 ATCC 49347 chromosome | CP026834.1 | Unannotated | 965436 | 966623 | x | 1,188 | 54, this study |
| Sd15_wzy | S. dysenteriae 15 ATCC 49347 chromosome | CP026834.1 | Unannotated | 966613 | 967854 | x | 1,242 | 54, this study |
| SdProv_wzx | S. dysenteriae provisional 96-265 chromosome | CP026819.1 | Unannotated | 2893541 | 2894860 | 1,320 | 54, this study | |
| SdProv_wzy | S. dysenteriae provisional 96-265 chromosome | CP026819.1 | Unannotated | 2899151 | 2900362 | 1,212 | 54, this study | |
| SdProvE_wzx | S. dysenteriae provisional E670-74 chromosome | CP027027.1 | Unannotated | 3878013 | 3879260 | x | 1,248 | 54, this study |
| SdProvE_wzy | S. dysenteriae provisional E670-74 chromosome | CP027027.2 | Unannotated | 3874004 | 3875176 | x | 1,173 | 54, this study |
| Sb1_wzx | S. boydii 1 O-Ag cluster | AY630255 | wzx | 4570 | 5754 | 1,185 | 49 | |
| Sb1_wzy | S. boydii 1 O-Ag cluster | AY630255 | wzy | 6605 | 7669 | 1,065 | 49 | |
| Sb2_wzx | S. boydii 2 O-Ag cluster | EU296418 | wzx | 4106 | 5353 | 1,248 | 10 | |
| Sb2_wzy | S. boydii 2 O-Ag cluster | EU296418 | wzy | 6127 | 7314 | 1,188 | 10 | |
| Sb3_wzx | S. boydii 3 O-Ag cluster | EU296407 | wzx | 1774 | 3039 | 1,266 | 10 | |
| Sb3_wzy | S. boydii 3 O-Ag cluster | EU296407 | wzy | 7165 | 8415 | 1,251 | 10 | |
| Sb4_wzx | S. boydii Sb227 chromosome | CP000036 | wzx | 877026 | 878255 | x | 1,230 | 43, 99 |
| Sb4_wzy | S. boydii Sb227 chromosome | CP000036 | wzy | 874635 | 875927 | x | 1,293 | 43, 99 |
| Sb5_wzx | S. boydii 5 O-Ag cluster | AF402313 | wzx | 7263 | 8411 | 1,149 | 43 | |
| Sb5_wzy | S. boydii 5 O-Ag cluster | AF402313 | wzy | 5379 | 6470 | 1,092 | 43 | |
| Sb6_wzx | S. boydii 6 O-Ag cluster | AF402314 | wzx | 11771 | 13183 | x | 1,413 | 43 |
| Sb6_wzy | S. boydii 6 O-Ag cluster | AF402314 | wzy | 3195 | 4247 | 1,053 | 43 | |
| WbaM | S. boydii 10 O-Ag cluster | AY693427 | wbaM | 9468 | 10424 | 957 | 48 | |
| Sb7_wzx | S. boydii 7 O-Ag cluster | EU296411 | wzx | 6714 | 7928 | 1,215 | 10 | |
| Sb7_wzy | S. boydii 7 O-Ag cluster | EU296411 | wzy | 8889 | 10184 | 1,296 | 10 | |
| Sb8_wzx | S. boydii 8 O-Ag cluster | EU294163 | wzx | 4664 | 5869 | 1,206 | 10 | |
| Sb8_wzy | S. boydii 8 O-Ag cluster | EU294163 | wzy | 7853 | 8935 | 1,083 | 10 | |
| Sb9_wzx | S. boydii 9 O-Ag cluster | AF402315 | wzx | 6944 | 8191 | 1,248 | 43 | |
| Sb9_wzy | S. boydii 9 O-Ag cluster | AF402315 | wzy | 4922 | 6139 | 1,218 | 43 | |
| Sb11_wzx | S. boydii 11 O-Ag cluster | AY529126 | wzx | 10367 | 11794 | x | 1,428 | 46 |
| Sb11_wzy | S. boydii 11 O-Ag cluster | AY529126 | wzy | 5432 | 6460 | 1,029 | 46 | |
| Sb12_wzx | S. boydii 12 O-Ag cluster | EU296406 | wzx | 6264 | 7580 | 1,317 | 10 | |
| Sb12_wzy | S. boydii 12 O-Ag cluster | EU296406 | wzy | 7561 | 8700 | 1,140 | 10 | |
| Sb13_wzx | S. boydii 13 O-Ag cluster | AY369140 | wzx | 1713 | 3032 | 1,320 | 44 | |
| Sb13_wzy | S. boydii 13 O-Ag cluster | AY369140 | wzy | 3019 | 4197 | 1,179 | 44 | |
| Sb14_wzx | S. boydii 14 O-Ag cluster | EU296409 | wzx | 1054 | 2511 | 1,458 | 10 | |
| Sb14_wzy | S. boydii 14 O-Ag cluster | EU296409 | wzy | 2515 | 3726 | 1,212 | 10 | |
| Sb15_wzx | S. boydii 15 O-Ag cluster | EU296412 | wzx | 1042 | 2433 | 1,392 | 10 | |
| Sb15_wzy | S. boydii 15 O-Ag cluster | EU296412 | wzy | 2453 | 3631 | 1,179 | 10 | |
| Sb16_wzx | S. boydii 16 O-Ag cluster | DQ371800 | wzx | 2385 | 3785 | 1,401 | 50 | |
| Sb16_wzy | S. boydii 16 O-Ag cluster | DQ371800 | wzy | 3796 | 4953 | 1,158 | 50 | |
| Sb17_wzx | S. boydii 17 O-Ag cluster | DQ875941 | wzx | 926 | 2191 | 1,266 | 51 | |
| Sb17_wzy | S. boydii 17 O-Ag cluster | DQ875941 | wzy | 4681 | 5892 | 1,212 | 51 | |
| Sb18_wzx | S. boydii CDC 3083-94 chromosome | CP001063 | wzx | 1103246 | 1104463 | 1,218 | 47, 54 | |
| Sb18_wzy | S. boydii CDC 3083-94 chromosome | CP001063 | wzy | 1105612 | 1106757 | 1,146 | 47, 54 | |
| Sb19_wzx | S. boydii 83-578 chromosome | CP026814.1 | Unannotated | 3586585 | 3587835 | 1,251 | 54, this study | |
| Sb19_wzx | S. boydii 83-578 chromosome | CP026814.1 | Unannotated | 3588633 | 3589772 | 1,140 | 54, this study | |
| SbProv_wzx | S. boydii provisional 54-1621 chromosome | CP026810 | Unannotated | 1495194 | 1496618 | 1,425 | 54, this This study | |
| SbProv_wzy | S. boydii provisional 54-1621 chromosome | CP026810 | Unannotated | 1499881 | 1501056 | 1,176 | 54, this This study | |
| Heparinase | E. coli isolate Co6114 plasmid pCo6114_2 | CP016036 | Heparinase II/III-like protein | 2803 | 4428 | x | 1,626 | This study |
| EclacY | E. coli DH1 (ME8569) chromosome | AP012030 | lacY | 362350 | 363603 | 1,254 | 100 | |
| cadA | S. dysenteriae 1 Sd197 chromosome | CP000034 | cadA | 4179987 | 4182129 | 2,143 | 99 | |
| Stx1 | S. dysenteriae 1 3818T Shiga toxin sequence | M19437 | stxA, stxB | 161 | 1387 | 1,227 | 62 | |
| Stx2 | E. coli O157:H7 EDL933 Stx2 sequence | X07865 | sltIIA, sltIIB | 239 | 1479 | 1,241 | 62 | |
| ShET1 | S. flexneri 2a 301 chromosome | AE005674.2 | set1B, set1A | 3069555 | 3070277 | 723 | 91, 101 | |
| ShET2 | S. sonnei pSS_046 | CP000039.1 | sen/ospD2 | 5491 | 7200 | x | 1,710 | 92, 102 |
| Sat_N | S. dysenteriae 10 ATCC 12039 chromosome | CP026831.1 | espC | 4214643 | 4217642 | 3,000 | 54, 103 |
a
Annotated reference genome sequences or O-antigen gene clusters based on which original characterization was published were chosen unless there was a mistake in the sequence (for example, EU118169 was chosen over EU294165, because the EU294165 differs from the rest of S. flexneri 6 O-antigen gene cluster sequences by 5 nucleotides). When annotation was not available, sequences were annotated by RAST (87–89) and serotype-specific determinants were identified. Publications from which the sequence was generated and the O-antigen gene cluster was characterized are included as references. Accession numbers refer to GenBank or SRA.