VIMSS Operon Predictions for Aquifex aeolicus VF5

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
 24294 24295 aq_001 aq_005 fusA tufA1 TRUE 0.998 17 1183.343
 24295 24296 aq_005 aq_008 tufA1 rpsJ TRUE 0.988 12 1030.566
 24296 24297 aq_008 aq_009 rpsJ rplC TRUE 0.987 5 2262.287
 24297 24298 aq_009 aq_011 rplC rplD TRUE 0.995 -3 2480.232
 24298 24299 aq_011 aq_012 rplD rplW TRUE 0.991 4 2504.37
 24299 24300 aq_012 aq_013 rplW rplB TRUE 0.995 12 2452.194
 24300 24301 aq_013 aq_015 rplB rpsS TRUE 0.801 113 2.485
 24301 24302 aq_015 aq_016a rpsS rplV FALSE 0.394 118 0
 24302 24303 aq_016a aq_017 rplV rpsC TRUE 0.976 3 367.249
 24303 24304 aq_017 aq_018 rpsC rplP TRUE 0.94 62 2575.844
 24304 24305 aq_018 aq_018a rplP rpmC TRUE 0.996 12 2121.092
 24305 24306 aq_018a aq_020 rpmC rpsQ TRUE 0.986 0 456.66
 24306 24307 aq_020 aq_021 rpsQ aroD FALSE 0.168 0 -0.059
 24308 24309 aq_022 aq_023 argD TRUE 0.67 12 -0.063
 24309 24310 aq_023 aq_024 argD nsd FALSE 0.177 -3 -4.029
 24310 24311 aq_024 aq_025 nsd rodA FALSE 0.189 278 -3.535
 24311 24312 aq_025 aq_025a rodA thiS FALSE 0.331 -31 -0.34
 24312 24313 aq_025a aq_026 thiS TRUE 0.59 -9 0
 24313 24314 aq_026 aq_027 FALSE 0.348 20 0
 24314 24315 aq_027 aq_028 FALSE 0.147 73 0
 24316 24317 aq_030 aq_031 moeA1 trnS TRUE 0.608 14 -2.413
 24317 24318 aq_031 aq_032 trnS FALSE 0.258 5 -1.436
 24320 24321 aq_036 aq_037 FALSE 0.24 113 0
 24321 24322 aq_037 aq_038 hibD TRUE 0.769 16 -0.023
 24323 24324 aq_039 aq_040 hisB TRUE 0.702 15 0
 24324 24325 aq_040 aq_041 FALSE 0.271 57 0
 24325 24326 aq_041 aq_042 cyc FALSE 0.338 33 0
 24326 24327 aq_042 aq_044 cyc petB TRUE 0.998 -3 91.211
 24327 24328 aq_044 aq_045 petB petA TRUE 0.987 14 1161.157
 24329 24330 aq_046 aq_049 pyrD phhB FALSE 0.18 8 -1.918
 24330 24331 aq_049 aq_050 phhB TRUE 0.524 -3 0
 24332 24333 aq_052 aq_053 ubiA mraY FALSE 0.18 -3 -3.711
 24333 24334 aq_053 aq_054 mraY FALSE 0.439 0 -0.133
 24337 24338 aq_057 aq_058 sfsA FALSE 0.266 497 0
 24338 24339 aq_058 aq_059 FALSE 0.239 122 0
 24341 24342 aq_062 aq_063 speE rpsF FALSE 0.039 75 -0.646
 24342 24343 aq_063 aq_064 rpsF ssb TRUE 0.973 -10 126.688
 24343 24344 aq_064 aq_064a ssb rpsR TRUE 0.931 19 96.833
 24344 24345 aq_064a aq_064b rpsR FALSE 0.053 55 -0.164
 24345 24346 aq_064b aq_064c TRUE 0.88 1 -0.035
 24349 24350 aq_067 aq_069 dmsB2 rplQ FALSE 0.039 233 -0.452
 24350 24351 aq_069 aq_070 rplQ rpoA TRUE 0.971 6 2496.361
 24351 24352 aq_070 aq_072 rpoA rpsD TRUE 0.979 13 1695.629
 24352 24353 aq_072 aq_073 rpsD rpsK TRUE 0.978 1 1713.243
 24353 24354 aq_073 aq_074 rpsK rpsM TRUE 0.993 16 2816.154
 24354 24355 aq_074 aq_075 rpsM rpmJ TRUE 0.993 -22 1569.443
 24355 24356 aq_075 aq_075a rpmJ infA TRUE 0.849 61 991.26
 24356 24357 aq_075a aq_076 infA map TRUE 0.969 3 417.821
 24357 24358 aq_076 aq_078 map kad TRUE 0.98 -10 457.494
 24358 24359 aq_078 aq_079 kad secY TRUE 0.964 5 1394.052
 24360 24361 aq_080 aq_081 rpmB aroC FALSE 0.116 0 -1.386
 24361 24362 aq_081 aq_082 aroC FALSE 0.148 2 -0.136
 24364 24365 aq_085 aq_086 kdsA modC FALSE 0.195 -3 -2.552
 24365 24366 aq_086 aq_087 modC FALSE 0.173 123 -0.006
 24366 24367 aq_087 aq_088 TRUE 0.955 15 4.913
 24367 24368 aq_088 aq_090 FALSE 0.454 28 0
 24368 24369 aq_090 aq_091m TRUE 0.584 -7 0
 24370 24371 aq_094 aq_097 nrdA FALSE 0.177 86 -0.008
 24372 24373 aq_098 aq_099 secG hemK FALSE 0.272 -64 -1.299
 24373 24374 aq_099 aq_101 hemK hly3 TRUE 0.692 -9 -0.245
 24375 24376 aq_103 aq_104 FALSE 0.198 3 -1.419
 24381 24382 aq_109 aq_111 glnB glnA TRUE 0.969 21 373.392
 24382 24383 aq_111 aq_112 glnA amtB TRUE 0.755 62 64.619
 24383 24384 aq_112 aq_113 amtB TRUE 0.958 14 4.522
 24385 24386 aq_114 aq_116 FALSE 0.25 317 0
 24386 24387 aq_116 aq_118 pgk FALSE 0.362 1 0
 24387 24388 aq_118 aq_119 pgk talC TRUE 0.873 12 -2.989
 24388 24389 aq_119 aq_121 talC FALSE 0.093 29 -0.4
 24389 24390 aq_121 aq_122 hisS1 FALSE 0.233 -3 -1.159
 24391 24392 aq_123 aq_124a rpsP TRUE 0.974 -3 43.474
 24392 24393 aq_124a aq_125 FALSE 0.454 0 -0.009
 24393 24394 aq_125 aq_126 TRUE 0.643 5 0
 24394 24395 aq_126 aq_127 TRUE 0.554 0 0
 24397 24398 aq_132 aq_133 ribH nusB TRUE 0.976 -3 1211.236
 24398 24399 aq_133 aq_134 nusB FALSE 0.168 202 -0.061
 24399 24400 aq_134 aq_135 nueM TRUE 0.637 -3 -0.128
 24400 24401 aq_135 aq_136 nueM cpx FALSE 0.134 23 -0.406
 24402 24403 aq_138 aq_139 ribD1 ribF TRUE 0.984 -3 -5.01
 24403 24404 aq_139 aq_141 ribF pkcI TRUE 0.7 7 -6.182
 24405 24406 aq_142 aq_145 rfaC2 TRUE 0.736 -3 0
 24406 24407 aq_145 aq_147 rfaC2 cobW TRUE 0.616 -3 -0.81
 24407 24408 aq_147 aq_148 cobW deoC TRUE 0.617 -3 -0.775
 24408 24409 aq_148 aq_150 deoC gltA FALSE 0.269 8 -0.064
 24409 24410 aq_150 aq_152 gltA tlpA TRUE 0.795 -3 0
 24410 24411 aq_152 aq_153 tlpA ctaA FALSE 0.342 580 0
 24411 24412 aq_153 aq_154 ctaA ctaB TRUE 0.985 -3 303.055
 24412 24413 aq_154 aq_155 ctaB FALSE 0.372 2 0
 24413 24414 aq_155 aq_156 FALSE 0.239 200 0
 24414 24415 aq_156 aq_157 FALSE 0.433 2 -0.004
 24415 24416 aq_157 aq_158 apfA TRUE 0.585 -3 -0.081
 24418 24419 aq_162 aq_164 folK ntrC4 FALSE 0.265 -3 -0.441
 24421 24422 aq_166 aq_167 proC TRUE 0.858 -39 -0.808
 24423 24424 aq_168 aq_169 TRUE 0.978 -45 0
 24424 24425 aq_169 aq_170 bioA FALSE 0.395 3 0
 24427 24428 aq_172 aq_173 mutY2 TRUE 0.858 -27 -0.034
 24428 24429 aq_173 aq_175 TRUE 0.699 -3 0
 24429 24430 aq_175 aqq_01 TRUE 0.971 -3 25.288
 24430 24431 aqq_01 aqq_02 rpmH TRUE 0.597 4 0
 24431 24432 aqq_02 aq_177 rpmH atpE FALSE 0.303 44 0
 24432 24433 aq_177 aq_178 atpE TRUE 0.665 16 0
 24433 24434 aq_178 aq_179 atpB TRUE 0.535 2 0
 24436 24437 aq_182 aq_183 TRUE 0.735 10 0
 24437 24438 aq_183 aq_183a rpoZ TRUE 0.736 -3 0
 24438 24439 aq_183a aq_184 rpoZ TRUE 0.658 -16 0
 24439 24440 aq_184 aq_185 tagD1 FALSE 0.147 335 0
 24440 24441 aq_185 aq_186 tagD1 aldH1 FALSE 0.27 -3 -0.398
 24441 24442 aq_186 aq_192 aldH1 hslU FALSE 0.05 11 -1.179
 24442 24443 aq_192 aq_194 hslU TRUE 0.788 -22 0
 24444 24445 aq_196 aq_197 trpD1 FALSE 0.39 0 0
 24445 24446 aq_197 aq_199 FALSE 0.259 66 0
 24446 24447 aq_199 aq_200 TRUE 0.651 -3 -0.016
 24447 24448 aq_200 aq_202 TRUE 0.629 -3 -0.291
 24448 24449 aq_202 aq_203 atpG2 TRUE 0.596 -16 0
 24451 24452 aq_206 aq_207 nirB cobA TRUE 0.626 16 -0.11
 24452 24453 aq_207 aq_209 cobA trpD2 TRUE 0.929 5 22.653
 24453 24454 aq_209 aq_211 trpD2 fhp FALSE 0.11 134 0
 24454 24455 aq_211 aq_212 fhp cynS FALSE 0.343 13 -0.012
 24455 24456 aq_212 aq_213 cynS glnBi FALSE 0.438 16 0
 24456 24457 aq_213 aq_215 glnBi nasA TRUE 0.524 -3 0
 24457 24458 aq_215 aq_217 nasA narB TRUE 0.962 -3 81.075
 24459 24460 aq_218 aq_220 nifA dut FALSE 0.185 17 -0.349
 24460 24461 aq_220 aq_221 dut phpA TRUE 0.966 -7 25.563
 24461 24462 aq_221 aq_226a phpA rpsO TRUE 0.975 3 2001.06
 24462 24463 aq_226a aq_227 rpsO aldH2 FALSE 0.043 59 -0.592
 24466 24467 aq_232 aq_234 dhsU soxF TRUE 0.638 10 -0.092
 24467 24468 aq_234 aq_235 soxF fccB' TRUE 0.856 -19 -0.122
 24470 24471 aq_238 aq_239 sodC2 folE FALSE 0.038 81 -0.66
 24474 24475 aq_243 aq_244 leuB TRUE 0.789 -13 0
 3290478 3315724 TRUE 0.525 1 0
 3315724 3290479 TRUE 0.525 1 0
 3290479 3315725 TRUE 0.525 1 0
 3315725 3290480 TRUE 0.525 1 0
 3290480 3332896 TRUE 0.525 1 0
 3332896 3331869 TRUE 0.525 1 0
 3331869 24476 aq_245 purK FALSE 0.243 90 0
 24477 24478 aq_246 aq_247 gatA FALSE 0.208 0 -0.703
 24478 24479 aq_247 aq_250 gatA TRUE 0.571 13 -0.698
 24479 24480 aq_250 aq_251 FALSE 0.258 47 0
 24480 24481 aq_251 aq_252 TRUE 0.665 16 0
 24481 24482 aq_252 aq_253 kdtB TRUE 0.788 -12 0
 24483 24484 aq_254 aq_255 FALSE 0.36 34 0
 24485 24486 aq_257 aq_259 ygcA nusA TRUE 0.979 -19 8.808
 24486 24487 aq_259 aq_260 nusA TRUE 0.987 -6 681.353
 24487 24488 aq_260 aq_262 FALSE 0.201 745 -0.053
 2209589 24489 aq_t01 aq_263 hemC TRUE 0.782 -45 0
 24489 24490 aq_263 aq_264 hemC TRUE 0.723 -3 -0.119
 24492 24493 aq_267 aq_268 FALSE 0.173 116 -0.005
 24495 24496 aq_270 aq_271 lgt TRUE 0.736 -3 0
 24498 24499 aq_273 aq_274 aspC4 FALSE 0.202 41 -1.833
 24500 24501 aq_276 aq_277 TRUE 0.65 -3 -0.026
 24501 24502 aq_277 aq_278 TRUE 0.736 -3 0
 24502 24503 aq_278 aq_281 acrR3 FALSE 0.465 25 0
 24505 24506 aq_283 aq_284 TRUE 0.974 -3 53.835
 24506 24507 aq_284 aq_286 FALSE 0.309 29 -0.78
 24507 24508 aq_286 aq_287 smb FALSE 0.418 0 -0.749
 24508 24509 aq_287 aq_288 smb FALSE 0.385 8 -0.022
 24510 24511 aq_291 aq_293 TRUE 0.68 11 -0.008
 24511 24512 aq_293 aq_294 TRUE 0.667 6 0
 24512 24513 aq_294 aq_296 TRUE 0.973 -3 98.416
 24513 24514 aq_296 aq_297 abcT8 TRUE 0.974 -7 170.775
 24517 24518 aq_302 aq_303 TRUE 0.957 -3 3.528
 24518 24519 aq_303 aq_305 ileS FALSE 0.294 -13 -1.023
 24521 24522 aq_311 aq_313 FALSE 0.453 -13 -0.436
 24522 24523 aq_313 aq_314 FALSE 0.355 9 -0.401
 24523 24524 aq_314 aq_316 hksP2 FALSE 0.053 109 -0.018
 24525 24526 aq_319 aq_321 phoB TRUE 0.923 11 -0.116
 24527 24528 aq_322 aq_323 dnaA FALSE 0.049 91 -0.071
 24533 24534 aq_328 aq_331 FALSE 0.421 30 0
 24534 2209590 aq_331 aq_t02 FALSE 0.291 48 0
 2209590 24535 aq_t02 aq_334 dcuP FALSE 0.487 26 0
 2209591 2209592 aq_t03 aq_t04 TRUE 0.76 12 0
 24537 24538 aq_337 aq_338 cysQ FALSE 0.138 4 -1.207
 24539 24540 aq_340 aq_341 FALSE 0.357 906 0
 24540 24541 aq_341 aq_342 TRUE 0.621 11 0
 24542 24543 aq_343 aq_344 arsA2 rfaD FALSE 0.297 -3 -0.132
 24545 24546 aq_346 aq_348 pth ctc TRUE 0.962 5 85.332
 24548 24549 aq_351 aq_355 leuS FALSE 0.419 4 -0.213
 24549 24550 aq_355 aq_356 leuA1 TRUE 0.555 14 -0.378
 24551 24552 aq_357a aq_358 flgM dinG FALSE 0.253 64 -0.047
 24552 24553 aq_358 aq_359 dinG TRUE 0.669 12 -0.074
 24554 24555 aq_360 aq_362 timA FALSE 0.461 336 0
 24555 24556 aq_362 aq_363 TRUE 0.554 0 0
 24556 24557 aq_363 aq_364 TRUE 0.641 -3 -0.074
 24557 24558 aq_364 aq_365 proS TRUE 0.795 -3 -3.833
 24559 3290481 aq_367 TRUE 0.702 15 0
 3290481 3315726 TRUE 0.525 1 0
 3315726 3290482 TRUE 0.525 1 0
 3290482 3315727 TRUE 0.525 1 0
 3315727 3290483 TR