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. 2013 Jun 20;8(6):e67510. doi: 10.1371/journal.pone.0067510

Table 1. Description of the sequences tiled on the PathogenID v2.0 microarray for the detection and characterization of BoNT-producing clostridia.

Tiled sequence description Species Type Strain Genbank accession no. Position (nt) length (nt)
Housekeeping genes
rrs 16S rRNA C. botulinum A1 DSM1734 X73442.1 7..1513 1506
rpoB RNA polymerase (subunit β) C. botulinum A1 NCTC7272 Y16466.1 1249..1755 506
rpoB RNA polymerase (subunit β) C. perfringens ATCC13124 CP000246.1 2986532..2986026 506
rpoB RNA polymerase (subunit β) C. difficile 630 AM180355.1 91744..92253 509
Neurotoxin complex genes
bont/A1 Botulinum neurotoxin type A1 C. botulinum A1 Hall AF461540.1 11250..11450 200
bont/A2 Botulinum neurotoxin type A2 C. botulinum A2 Kyoto X73423.1 1771..1971 200
bont/B1 Botulinum neurotoxin type B1 C. botulinum B1 Okra AB232927.1 14210..14410 200
bont/Bnp Botulinum neurotoxin type Bnp C. botulinum Bnp ATCC25765 X71343.1 3586..3786 200
bont/C1 Botulinum neurotoxin type C1 C. botulinum C1 468 X53751.1 1876..2076 200
bont/D Botulinum neurotoxin type D C. botulinum D 1873 X54254.1 1697..1897 200
bont/E Botulinum neurotoxin type E C. botulinum E1 Beluga X62089.1 1213..1413 200
bont/F Botulinum neurotoxin type F C. botulinum F6 202 M92906.1 606..806 200
bont/G Botulinum neurotoxin type G C. botulinum G NCFB3012 X74162.1 1651..1851 200
ntnh/A1 Non-toxigenic non-hemagglutinin C. botulinum A1 Hall AF461540 8501..8695 194
ntnh/A2 Non-toxigenic non-hemagglutinin C. botulinum A2 Kyoto X87974 2453..2647 194
ntnh/A3 Non-toxigenic non-hemagglutinin C. botulinum A3 Mascarpone DQ310546 5690..5884 194
ntnh/Bp Non-toxigenic non-hemagglutinin C. botulinum B1 Okra AB232927 9649..9843 194
ntnh/C Non-toxigenic non-hemagglutinin C. botulinum C1 468 X72793 4757..4966 209
ntnh/D Non-toxigenic non-hemagglutinin C. botulinum D 1873 AB012112 4483..4692 209
ntnh/E Non-toxigenic non-hemagglutinin C. botulinum E Mashike D12697 2644..2838 194
ntnh/Ebut Non-toxigenic non-hemagglutinin C. butyricum E4 BL6340 D12739 2644..2838 194
ntnh/F Non-toxigenic non-hemagglutinin C. botulinum F6 202 S73676 2664..2858 194
ntnh/G Non-toxigenic non-hemagglutinin C. botulinum G ATCC27322 X87972 3390..3599 209
ha17/A Hemagglutinin 17 C. botulinum A1 Hall AF461540 4022..3822 200
ha17/Bp Hemagglutinin 17 C. botulinum B1 Okra AB232927 5170..4970 200
ha17/C Hemagglutinin 17 C. botulinum C1 468 X72793 3181..2981 200
ha17/D Hemagglutinin 17 C. botulinum D 1873 AB012112 2907..2707 200
ha17/G Hemagglutinin 17 C. botulinum G ATCC27322 X87972 1749..1600 149
ha70/A Hemagglutinin 70 C. botulinum A Hall AF461540 3166..3005 161
ha70/Bp Hemagglutinin 70 C. botulinum B1 Okra AB232927 4314..4153 161
ha70/C/D Hemagglutinin 70 C. botulinum C1 468 X72793 2337..2173 164
ha70/G Hemagglutinin 70 C. botulinum G ATCC27322 X87972 945..787 158
ha33/A Hemagglutinin 33 C. botulinum A1 Hall AF461540 4603..4403 200
ha33/Bp Hemagglutinin 33 C. botulinum B1 Okra AB232927 5748..5548 200
ha33/C/D Hemagglutinin 33 C. botulinum C1 468 X72793 3750..3550 200
orfX1/A2 Orf-X component 1 C. botulinum A2 Kyoto AB004778 524..315 209
orfX1/A3 Orf-X component 1 C. botulinum A3 Mascarpone DQ310546 1001..792 209
orfX1/E Orf-X component 1 C. botulinum E Iwanai D88418 1046..837 209
orfX2/A2 Orf-X component 2 C. botulinum A2 Kyoto AY497358 4619..4373 246
orfX2/E Orf-X component 2 C. botulinum E Iwanai D88418 256..10 246
orfX3/A2 Orf-X component 3 C. botulinum A2 Kyoto AY497358 2445..2236 209
botR/A1 Transcriptionnal regulator BotR C. botulinum A1 Hall AF461540 5502..5702 200
botR/A2 Transcriptionnal regulator BotR C. botulinum A2 Kyoto X96493 229..29 200
botR/A3 Transcriptionnal regulator BotR C. botulinum A3 Mascarpone DQ310546 1438..1238 200
botR/B Transcriptionnal regulator BotR C. botulinum B1 Okra AB232927 6653..6853 200
botR/C Transcriptionnal regulator BotR C. botulinum C1 468 X72793 512..712 200
botR/D Transcriptionnal regulator BotR C. botulinum D 1873 AB012112 238..438 200
botR/G Transcriptionnal regulator BotR C. botulinum G ATCC27322 X87972 2595..2795 200
p47/A2 P 47 C. botulinum A2 Kyoto X96493 779..937 158
p47/A3 P 47 C. botulinum A3 Mascarpone DQ310546 1976..2134 158
p47/E P 47 C. botulinum E Iwanai D88418 1881..2081 200
p47/F P 47 C. botulinum F6 202 Y10770 946..1116 170
Clostridial toxin genes
C2 C2 toxin (component 1) C. botulinum (C)-203U28 D88982.1 838..1038 200
C2 C2 toxin (component 2) C. botulinum (C)-203U28 D88982.1 2245..2445 200
tent Tetanus neurotoxin C. tetani Massachusetts X04436.1 2026..2226 200
toxB Toxin B C. difficile VPI10463 X53138.1 1518..1718 200
toxB Toxin BF C. difficile 1470 Z23277.1 1183..1383 200
toxA Toxin A C. difficile VPI10463 X51797.1 2521..2721 200
cpa α-toxin C. perfringens S13 L43546.1 1317..1517 200
cpb1 β-toxin C. perfringens NCTC 8533 L13198.1 510..710 200
cpb2 β2-toxin C. perfringens Porcine CWC245 L77965.1 418..618 200
cpb2 β2-toxin C. perfringens Equine D21/98 AJ537535.1 199..399 200
cpb2 β2-toxin C. perfringens Bovine JGS4147 AY609175 151..351 200
etxD ε-toxin D C. perfringens NCTC 8346 M95206.1 714..914 200
pfoR τ-toxin (perfringolysin) C. perfringens lambda gt10 M81080.1 3529..3729 200
enterotoxin Enterotoxin C. perfringens NCTC8239 M98037.1 787..987 200
toxin-iota-a ι-toxin (component Ia) C. perfringens NCIB10748 X73562.1 2254..2454 200
toxin-iota-b ι-toxin (component Ib) C. perfringens NCIB10748 X73562.1 3515..3715 200
toxin-LT82 Lethal toxin 82 C. sordellii 82 X82638.1 1595..1795 200
α-toxin α-toxin C. septicum NCTC547 D17668.1 1062..1262 200
α-toxin α-novyi toxin C. oedematiens ATCC19402 Z48636.1 1286..1486 200
Quinolone-resistance determining regions
gyrA-qrdr Gyrase (subunit A) C. perfringens ATCC13124 CP000246.1 7269..7466 197
gyrA-qrdr Gyrase (subunit A) C. difficile 630 AM180355.1 6231..6428 197
parC-qrdr Topoisomerase (subunit IV) C. perfringens SM101 CP000312.1 2254972..2255160 188