VIMSS Operon Predictions for Bordetella pertussis Tohama I

For each pair of adjacent genes on the same strand, we report whether they are predicted to be in the same operon, and the two most important features. Small plasmids and, in draft genomes, small scaffolds, are excluded.

Also see:

Column Description
Gene1 VIMSS id of 1st gene in pair
SysName1 Systematic name of 1st gene in pair
Name1 Ordinary name of 1st gene in pair
Gene2 VIMSS id of 2nd gene in pair
SysName2 Systematic name of 2nd gene in pair
Name2 Ordinary name of 2nd gene in pair
bOp Whether the pair is predicted to lie in the same operon or not
pOp Estimated probability that the pair is in the same operon. Values near 1 or 0 are confident predictions of being in the same operon or not, while values near 0.5 are low-confidence predictions.
Sep Distance between the two genes, in base pairs
GNMinus An indicator of conservation (gene neighbor score, surprisal subtracted). Positive scores indicate conservation, and scores above 5 are generally strongly indicative of operons

 Gene1 Gene2 SysName1 SysName2 Name1 Name2 bOp pOp Sep GNMinus
 511295 511296 BP0001 BP0002 gidA gidB TRUE 0.994 -3 540.768
 511296 511297 BP0002 BP0003 gidB parA TRUE 0.992 -3 417.478
 511297 511298 BP0003 BP0004 parA TRUE 0.747 7 -2.181
 511298 511299 BP0004 BP0005 parB FALSE 0.406 44 -1.848
 511299 511300 BP0005 BP0006 parB ansB TRUE 0.675 -7 0
 511300 511301 BP0006 BPt01 ansB FALSE 0.106 110 0
 511301 511302 BPt01 BPt02 FALSE 0.047 189 0
 511302 511303 BPt02 BPt03 TRUE 0.748 7 0
 511303 511304 BPt03 BP0007 tufA FALSE 0.303 57 0
 511304 511305 BP0007 BPt04 tufA FALSE 0.106 111 0
 511305 511306 BPt04 BP0008 secE FALSE 0.345 53 0
 511306 511307 BP0008 BP0009 secE nusG TRUE 0.985 10 219.182
 511307 511308 BP0009 BP0010 nusG rplK TRUE 0.959 64 1163.023
 511308 511309 BP0010 BP0011 rplK rplA TRUE 0.999 3 1516.354
 511309 511310 BP0011 BP0013 rplA rplJ TRUE 0.853 243 1135.312
 511310 511311 BP0013 BP0014 rplJ rplL TRUE 0.978 82 1522.898
 511311 511312 BP0014 BP0015 rplL rpoB TRUE 0.621 160 824.583
 511312 511313 BP0015 BP0016 rpoB rpoC TRUE 0.998 0 828.658
 511316 511317 BP0019 BP0020 TRUE 0.764 2 0
 511317 511318 BP0020 BP0021 TRUE 0.619 18 0
 511320 511321 BP0023 BP0024 FALSE 0.142 82 0
 511321 511322 BP0024 BP0025 TRUE 0.553 25 0
 511322 511323 BP0025 BP0026 TRUE 0.776 33 6.186
 511323 511324 BP0026 BP0027 TRUE 0.956 -3 2.225
 511324 511325 BP0027 BP0028 FALSE 0.023 208 -0.747
 511326 511327 BP0029 BP0030 TRUE 0.55 43 0.042
 511327 511328 BP0030 BP0031 FALSE 0.071 156 0
 511330 511331 BP0033 BP0034 glyQ glyS TRUE 0.999 2 854.382
 511331 511332 BP0034 BP0035 glyS TRUE 0.98 -3 98.3
 511332 511333 BP0035 BP0036 TRUE 0.986 4 119.068
 511333 511334 BP0036 BP0037 TRUE 0.94 -13 53.942
 511334 511335 BP0037 BP0038 gloA TRUE 0.599 71 33.702
 511335 511336 BP0038 BP0039 gloA TRUE 0.666 10 -17.842
 511344 511345 BP0047 BP0048 metX TRUE 0.992 -3 260.24
 511345 511346 BP0048 BP0049 FALSE 0.085 136 0
 511346 511347 BP0049 BP0050 ampG FALSE 0.15 88 0
 511347 511348 BP0050 BP0051 ampG FALSE 0.106 112 0
 511349 511350 BP0053 BP0054 gltL TRUE 0.75 6 0
 511350 511351 BP0054 BP0055 gltL gltK TRUE 0.553 25 0
 511351 511352 BP0055 BP0056 gltK gltJ TRUE 0.996 -3 225.582
 511352 511353 BP0056 BP0057 gltJ TRUE 0.963 47 67.827
 511353 511354 BP0057 BP0058 FALSE 0.141 94 0
 511356 511357 BP0060 BP0061 TRUE 0.933 0 16.546
 511357 511358 BP0061 BP0062 FALSE 0.067 184 0.029
 511358 511359 BP0062 BP0063 FALSE 0.01 424 0.029
 511359 511360 BP0063 BP0064 FALSE 0.084 195 0.042
 511360 511361 BP0064 BP0065 TRUE 0.796 13 -0.23
 511361 511362 BP0065 BP0066 FALSE 0.323 119 0.042
 511362 511363 BP0066 BP0067 TRUE 0.529 32 0.013
 511363 511364 BP0067 BP0068 FALSE 0.106 109 0
 511364 511365 BP0068 BP0069 FALSE 0.274 61 0
 511365 511366 BP0069 BP0070 TRUE 0.587 21 0
 511367 511368 BP0071 BP0072 FALSE 0.117 94 0
 511368 511369 BP0072 BP0073 TRUE 0.742 -3 0
 511372 511373 BP0075 BP0076 ampD FALSE 0.356 32 -10.966
 511373 511374 BP0076 BP0077 ampD FALSE 0.096 89 -6.557
 511374 511375 BP0077 BP0078 TRUE 0.911 2 6.368
 511377 511379 BP0080 BP0082 bplL FALSE 0.011 1016 0
 511379 511380 BP0082 BP0083 bplL bplJ FALSE 0.378 49 0
 511380 511381 BP0083 BP0085 bplJ bplI TRUE 0.675 -7 0
 511381 511382 BP0085 BP0086 bplI bplH TRUE 0.689 -3 -0.801
 511382 511383 BP0086 BP0087 bplH bplG FALSE 0.251 196 -1.559
 511383 511384 BP0087 BP0088 bplG bplF TRUE 0.991 -3 70.899
 511384 511385 BP0088 BP0089 bplF bplE TRUE 0.918 18 -1.939
 511385 511386 BP0089 BP0090 bplE bplD TRUE 0.954 24 35.176
 511386 511387 BP0090 BP0091 bplD bplC TRUE 0.987 8 -2.715
 511387 511388 BP0091 BP0092 bplC bplB TRUE 0.986 4 65.735
 511388 511389 BP0092 BP0093 bplB bplA TRUE 0.96 4 14.234
 511390 511391 BP0094 BP0095 rfaC kdtA TRUE 0.984 2 81.472
 511392 511393 BP0096 BP0097 baf TRUE 0.618 25 0.013
 511393 511394 BP0097 BP0098 baf birA TRUE 0.978 -3 87.383
 511395 511396 BP0099 BP0100 TRUE 0.995 0 252.104
 511396 511397 BP0100 BP0101 TRUE 0.658 -13 0
 511397 511398 BP0101 BP0101A TRUE 0.764 1 0
 511398 511399 BP0101A BP0101B FALSE 0.391 30 -20.315
 511399 511400 BP0101B BP0102 FALSE 0.242 133 35.376
 511400 511401 BP0102 BP0103 TRUE 0.878 48 55.753
 511401 511402 BP0103 BP0104 TRUE 0.685 76 56.497
 511402 511403 BP0104 BP0105 lipB TRUE 0.963 8 200.259
 511403 511404 BP0105 BP0106 lipB lipA TRUE 0.988 62 361.351
 511405 511406 BP0107 BP0108 rfbC rfbD TRUE 0.974 58 438.632
 511406 511407 BP0108 BP0109 rfbD rfbB TRUE 0.998 -3 495.101
 511407 511408 BP0109 BP0110 rfbB TRUE 0.513 36 0
 511408 511409 BP0110 BP0111 FALSE 0.106 99 0
 511411 511412 BP0113 BP0114 dsbA TRUE 0.793 62 65.618
 511412 511413 BP0114 BP0115 argS TRUE 0.978 10 79.781
 511414 511415 BP0116 BP0117 FALSE 0.295 49 -3.522
 511415 511416 BP0117 BP0118 FALSE 0.02 283 0
 511417 511418 BP0119 BP0120 TRUE 0.995 -3 147.433
 511418 511419 BP0120 BP0121 TRUE 0.994 11 109.462
 511419 511420 BP0121 BP0122 TRUE 0.933 43 20.863
 511420 511421 BP0122 BP0123 FALSE 0.357 106 1.701
 511421 511422 BP0123 BP0125 TRUE 0.569 23 0
 511422 511423 BP0125 BP0124 TRUE 0.645 -1028 0
 511423 511424 BP0124 BP0126 FALSE 0.012 1001 0
 511424 511425 BP0126 BP0127 TRUE 0.742 -3 0
 511425 511426 BP0127 BP0128 TRUE 0.764 2 0
 511426 511427 BP0128 BP0129 TRUE 0.742 -3 0
 511429 511430 BP0131 BP0132 leuA FALSE 0.01 427 0.042
 511431 511432 BP0133 BP0134 rpoN FALSE 0.074 93 -1.81
 511438 511439 BP0140 BP0141 FALSE 0.048 187 0
 511439 511440 BP0141 BP0142 FALSE 0.453 53 0.042
 511441 511442 BP0143 BP0144 TRUE 0.811 -16 -1.177
 511442 511443 BP0144 BP0145 TRUE 0.968 6 -0.884
 511443 511444 BP0145 BP0146 TRUE 0.587 21 0
 511444 511445 BP0146 BP0148 FALSE 0.213 72 0
 511447 511448 BP0150 BP0151 TRUE 0.742 -3 0
 511448 511449 BP0151 BP0152 TRUE 0.995 -3 430.247
 511449 511450 BP0152 BP0153 TRUE 0.544 25 -5.521
 511452 511453 BP0155 BP0156 serA FALSE 0.098 84 -10.177
 511453 511454 BP0156 BP0157 FALSE 0.086 106 -9.116
 511454 511455 BP0157 BP0158 TRUE 0.996 -3 188.173
 511455 511456 BP0158 BP0159 phoR TRUE 0.648 56 -17.058
 511456 511457 BP0159 BP0160 phoR phoB TRUE 0.996 12 342.848
 511458 511459 BP0161 BP0162 ubiE FALSE 0.32 166 44.02
 511459 511460 BP0162 BP0163 FALSE 0.216 178 36.199
 511460 511461 BP0163 BP0164 ubiB TRUE 0.977 -3 231.28
 511461 511462 BP0164 BP0165 ubiB FALSE 0.056 175 0
 511465 511466 BP0168 BP0169 TRUE 0.986 -22 356.304
 511467 511468 BP0170 BP0171 rhlE FALSE 0.408 34 -10.709
 511468 511469 BP0171 BP0172 prfC FALSE 0.493 25 -12.38
 511469 511470 BP0172 BP0173 prfC TRUE 0.683 25 0.042
 511474 511475 BP0177 BP0178 FALSE 0.441 92 0.042
 511475 511476 BP0178 BP0179 FALSE 0.215 61 -2.357
 511477 511478 BP0180 BP0181 metG FALSE 0.045 250 0.042
 511479 511480 BP0182 BP0183 TRUE 0.71 4 -4.605
 511480 511481 BP0183 BP0184 TRUE 0.936 -3 17.227
 511481 511482 BP0184 BP0185 dcd FALSE 0.226 61 -2.797
 511483 511484 BP0186 BP0187 FALSE 0.444 28 -1.954
 511484 511485 BP0187 BP0188 TRUE 0.515 29 0
 511486 511487 BP0189 BP0190 FALSE 0.092 155 0.013
 511487 511488 BP0190 BP0191 FALSE 0.289 49 -18.436
 511488 511489 BP0191 BP0192 FALSE 0.106 99 0
 511489 511490 BP0192 BP0193 sodA FALSE 0.125 103 0
 511490 511491 BP0193 BP0194 sodA TRUE 0.976 -3 11.282
 511491 511492 BP0194 BP0195 gcvT FALSE 0.009 395 -10.321
 511492 511493 BP0195 BP0196 gcvT gcvH TRUE 0.984 82 711.398
 511493 511494 BP0196 BP0197 gcvH gcvP TRUE 0.96 60 489.733
 511496 511497 BP0199 BP0200 TRUE 0.513 29 -0.342
 511497 511498 BP0200 BP0201 TRUE 0.742 -3 0
 511498 511499 BP0201 BP0202 FALSE 0.106 99 0
 511500 511501 BP0202A BP0203 FALSE 0.128 87 0
 511501 511502 BP0203 BP0204 FALSE 0.106 115 0
 511502 511503 BP0204 BP0205 FALSE 0.121 91 0
 511505 511506 BP0207 BP0208 FALSE 0.319 113 -9.35
 511506 511507 BP0208 BP0209 TRUE 0.808 17 1.846
 511508 511509 BP0210 BP0211 FALSE 0.195 99 0
 511513 511514 BP0215 BP0216 ppc sphB1 FALSE 0.009 591 -2.249
 511514 511515 BP0216 BP0217 sphB1 FALSE 0.01 458 -0.151
 511515 511516 BP0217 BP0218 FALSE 0.331 112 -0.859
 511516 511517 BP0218 BP0219 TRUE 0.722 32 1.796
 511519 511520 BP0221 BP0222 catI catJ TRUE 0.998 0 136.229
 511520 511521 BP0222 BP0223 catJ catC2 FALSE 0.425 57 -6.263
 511521 511522 BP0223 BP0224 catC2 FALSE 0.458 26 -3.339
 511522 511523 BP0224 BP0225 catD2 FALSE 0.313 46 -5.243
 511523 511524 BP0225 BP0226 catD2 TRUE 0.678 -3 -0.386
 511525 511526 BP0227 BP0228 psiF FALSE 0.07 157 0
 511526 511527 BP0228 BP0229 FALSE 0.128 99 0
 511527 511528 BP0229 BP0230 TRUE 0.742 -3 0
 511529 511530 BP0231 BP0232 pcaC FALSE 0.323 55 0
 511531 511532 BP0233 BP0234 FALSE 0.483 44 -0.027
 511533 511534 BP0235 BP0236 TRUE 0.742 -3 0
 511534 511535 BP0236 BP0237 TRUE 0.532 27 0
 511536 511537 BP0238 BP0239 folK pcnB TRUE 0.988 -3 319.153
 511537 511538 BP0239 BP0240 pcnB TRUE 0.952 1 39.774
 511538 511539 BP0240 BP0241 TRUE 0.963 -3 48.57
 511541 511542 BP0243 BP0244 miaA mutL TRUE 0.992 -3 311.087
 511544 511545 BP0246 BP0247 amiC TRUE 0.828 72 140.227
 511551 511552 BP0253 BP0254 TRUE 0.867 14 5.354
 511552 511553 BP0254 BP0255 FALSE 0.459 36 0
 511554 511555 BP0256 BP0257 TRUE 0.765 0 0
 511555 511556 BP0257 BP0258 FALSE 0.056 174 0
 511556 511557 BP0258 BP0259 cydA FALSE 0.161 84 -1.715
 511557 511558 BP0259 BP0260 cydA cydB TRUE 0.996 16 646.262
 511558 511559 BP0260 BP0261 cydB TRUE 0.926 14 22.641
 511559 511560 BP0261 BP0262 TRUE 0.856 -3 -0.544
 511560 511561 BP0262 BP0263 TRUE 0.997 -3 450.918
 511561 511562 BP0263 BP0264 apt FALSE 0.364 63 -16.229
 511564 511565 BP0266 BP0267 FALSE 0.036 210 0
 511567 511568 BP0270 BP0271 TRUE 0.745 8 0
 511569 511570 BPt06 BP0273 sspB FALSE 0.169 78 0
 511570 511571 BP0273 BP0274 sspB sspA TRUE 0.986 10 312.293
 511571 511572 BP0274 BP0275 sspA petC TRUE 0.573 159 188.02
 511572 511573 BP0275 BP0276 petC petB TRUE 0.997 26 406.911
 511573 511574 BP0276 BP0277 petB petA TRUE 0.984 65 492.775
 511578 511579 BP0281 BP0282 FALSE 0.106 99 0
 511579 511580 BP0282 BP0283 FALSE 0.466 23 -0.464
 511580 511581 BP0283 BP0284