VIMSS Operon Predictions for Bdellovibrio bacteriovorus HD100

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
 1762278 1762279 Bd0001 Bd0002 dnaA dnaN TRUE 0.91 233 858.418
 1762279 1762280 Bd0002 Bd0003 dnaN TRUE 0.996 0 1016.537
 1762280 1762281 Bd0003 Bd0004 TRUE 0.972 87 631.062
 1762281 1762282 Bd0004 Bd0005 gyrA TRUE 0.989 24 101.642
 1762282 1762283 Bd0005 Bd0006 gyrA TRUE 0.608 2 0
 1762283 1762284 Bd0006 Bd0007 TRUE 0.617 0 0
 1762284 1762285 Bd0007 Bd0008 TRUE 0.621 -3 0
 1762285 1762286 Bd0008 Bd0009 atpB TRUE 0.613 -10 0
 1762286 1762287 Bd0009 Bd0010 atpB atpE/H TRUE 0.951 33 13.667
 1762289 1762290 Bd0012 Bd0013 FALSE 0.234 44 0
 1762291 1762292 Bd0014 Bd0015 pmm pdxA FALSE 0.415 48 -5.213
 1762292 1762293 Bd0015 Bd0017 pdxA surA TRUE 0.98 -7 16.552
 1762293 1762294 Bd0017 Bd0018 surA ppiC TRUE 0.972 14 6.37
 1762294 1762295 Bd0018 Bd0019 ppiC ppiD TRUE 0.971 13 2.873
 1762295 1762296 Bd0019 Bd0020 ppiD FALSE 0.206 48 -0.278
 1762296 1762297 Bd0020 Bd0021 etfA TRUE 0.607 3 -0.596
 1762297 1762298 Bd0021 Bd0022 etfA etfB TRUE 0.997 11 1027.403
 1762299 1762300 Bd0024 Bd0025 sdhC sdhA TRUE 0.989 12 220.307
 1762300 1762301 Bd0025 Bd0026 sdhA sdhB TRUE 0.996 11 325.608
 1762301 1762302 Bd0026 Bd0027 sdhB FALSE 0.061 301 0
 1762302 1762303 Bd0027 Bd0028 FALSE 0.496 12 0
 1762303 1762304 Bd0028 Bd0029 FALSE 0.085 107 0
 1762305 1762306 Bd0030 Bd0031 pcbD FALSE 0.426 12 -0.053
 1762307 1762308 Bd0032 Bd0033 rpsF TRUE 0.925 20 14.83
 1762308 1762309 Bd0033 Bd0034 rplI TRUE 0.939 17 19.309
 1762309 1762310 Bd0034 Bd0035 rplI FALSE 0.101 172 -0.181
 1762311 1762312 Bd0036 Bd0037 FALSE 0.077 115 0
 1762312 1762313 Bd0037 Bd0038 dnaB TRUE 0.572 15 -6.294
 1762313 1762314 Bd0038 Bd0039 dnaB fis FALSE 0.424 103 -3.429
 1762314 1762315 Bd0039 Bd0040 fis FALSE 0.441 36 -2.185
 1762316 1762317 Bd0041 Bd0042 ftsK FALSE 0.154 73 0
 1762317 1762318 Bd0042 Bd0043 TRUE 0.598 4 0
 1762318 1762319 Bd0043 Bd0044 TRUE 0.61 -16 0
 1762319 1762320 Bd0044 Bd0045 dapF TRUE 0.621 -3 0
 1762320 1762321 Bd0045 Bd0046 dapF dapA TRUE 0.961 -3 -2.998
 1762321 1762322 Bd0046 Bd0047 dapA dapB TRUE 0.995 -3 161.447
 1762322 1762323 Bd0047 Bd0048 dapB TRUE 0.621 -3 0
 1762323 1762324 Bd0048 Bd0049 talC FALSE 0.181 62 0
 1762324 1762325 Bd0049 Bd0050 talC TRUE 0.617 0 0
 1762325 1762326 Bd0050 Bd0051 FALSE 0.219 50 0
 1762328 1762329 Bd0054 Bd0055 FALSE 0.103 94 0
 1762329 1762330 Bd0055 Bd0056 FALSE 0.085 107 0
 1762332 1762333 Bd0058 Bd0059 gatC gatA TRUE 0.998 10 1063.923
 1762333 1762334 Bd0059 Bd0060 gatA gatB TRUE 0.998 -10 864.291
 1762334 1762335 Bd0060 Bd0061 gatB TRUE 0.626 16 -8.9
 1762335 1762336 Bd0061 Bd0062 TRUE 0.571 8 -0.426
 1762336 1762337 Bd0062 Bd0063 FALSE 0.11 90 0
 1762341 1762342 Bd0068 Bd0069 rpmE prfA TRUE 0.867 148 86.831
 1762342 1762343 Bd0069 Bd0070 prfA hemK TRUE 0.996 4 1376.979
 1762343 1762344 Bd0070 Bd0071 hemK murA TRUE 0.978 2 5.852
 1762345 1762346 Bd0072 Bd0073 FALSE 0.121 134 0
 1762346 1762347 Bd0073 Bd0074 FALSE 0.064 142 0
 1762348 1762349 Bd0075 Bd0076 FALSE 0.298 28 0
 1762349 1762350 Bd0076 Bd0077 serS FALSE 0.274 33 0
 1762350 1762351 Bd0077 trna_0001 serS FALSE 0.099 97 0
 1762351 1762352 trna_0001 Bd0078 FALSE 0.071 125 0
 1762352 1762353 Bd0078 Bd0080 dedA TRUE 0.584 7 0
 1762354 1762355 Bd0081 Bd0082 cyaB TRUE 0.61 -16 0
 1762356 1762357 Bd0083 Bd0084 TRUE 0.553 10 0
 1762357 1762358 Bd0084 Bd0085 FALSE 0.175 64 0
 1762358 1762359 Bd0085 Bd0086 FALSE 0.373 17 0
 1762359 1762360 Bd0086 Bd0087 FALSE 0.2 56 0
 1762360 1762361 Bd0087 Bd0088 FALSE 0.06 231 0
 1762361 1762362 Bd0088 Bd0089 FALSE 0.129 82 0
 1762362 1762363 Bd0089 Bd0090 FALSE 0.06 222 0
 1762367 1762368 Bd0092 Bd0093 TRUE 0.921 25 17.538
 1762368 1762369 Bd0093 Bd0094 FALSE 0.212 52 0
 1762369 1762370 Bd0094 trna_0004 FALSE 0.192 58 0
 1762370 1762371 trna_0004 Bd0095 FALSE 0.087 106 0
 1762371 1762372 Bd0095 Bd0096 TRUE 0.58 8 0
 1762372 1762373 Bd0096 Bd0097 groES FALSE 0.061 161 0
 1762373 1762374 Bd0097 Bd0099 groES groEL TRUE 0.988 57 1539.8
 1762376 1762377 Bd0101 Bd0102 cheY FALSE 0.237 43 0
 1762377 1762378 Bd0102 Bd0103 cheY TRUE 0.611 -13 0
 1762379 1762380 Bd0108 Bd0109 FALSE 0.396 16 0
 1762380 1762381 Bd0109 Bd0110 TadB FALSE 0.283 31 0
 1762381 1762382 Bd0110 Bd0111 TadB TadA TRUE 0.907 4 0
 1762382 1762383 Bd0111 Bd0112 TadA PilQ TRUE 0.601 53 0
 1762383 1762384 Bd0112 Bd0113 PilQ CpaB TRUE 0.675 35 0
 1762384 1762385 Bd0113 Bd0114 CpaB FALSE 0.361 18 0
 1762385 1762386 Bd0114 Bd0115 TRUE 0.616 -6 0
 1762386 1762387 Bd0115 Bd0117 TRUE 0.553 10 0
 1762387 1762388 Bd0117 Bd0118 TRUE 0.621 -3 0
 1762388 1762389 Bd0118 Bd0119 FALSE 0.216 51 0
 1762389 1762390 Bd0119 Bd0120 FALSE 0.062 154 0
 1762390 1762391 Bd0120 Bd0121 TRUE 0.523 11 0
 1762391 1762392 Bd0121 Bd0122 hprT FALSE 0.112 299 0
 1762392 1762393 Bd0122 Bd0123 hprT TRUE 0.612 13 -0.246
 1762393 1762394 Bd0123 Bd0125 comL TRUE 0.986 0 12.469
 1762394 1762395 Bd0125 Bd0126 comL TRUE 0.559 35 -0.069
 1762396 1762397 Bd0127 Bd0129 argD dapE TRUE 0.908 1 -0.244
 1762397 1762398 Bd0129 Bd0130 dapE astA TRUE 0.917 -3 -0.924
 1762398 1762399 Bd0130 Bd0131 astA astD TRUE 0.989 4 496.606
 1762399 1762400 Bd0131 Bd0132 astD TRUE 0.867 0 -3.628
 1762402 1762403 Bd0134 Bd0135 lysC FALSE 0.419 49 -7.977
 1762403 1762404 Bd0135 Bd0136 FALSE 0.142 233 -9.179
 1762404 1762405 Bd0136 Bd0137 typA FALSE 0.173 123 -30.185
 1762405 1762406 Bd0137 Bd0138 typA nodI TRUE 0.808 0 -11.833
 1762406 1762407 Bd0138 Bd0139 nodI nodJ TRUE 0.989 0 268.187
 1762408 1762409 Bd0140 Bd0141 TRUE 0.69 -3 0
 1762409 1762410 Bd0141 Bd0142 dfrA TRUE 0.592 8 -0.035
 1762410 1762411 Bd0142 Bd0143 dfrA TRUE 0.697 -3 -0.829
 1762412 1762413 Bd0144 Bd0145 motA motB TRUE 0.99 15 413.131
 1762414 1762415 Bd0146 Bd0147 bglX2 TRUE 0.598 4 0
 1762416 1762417 Bd0148 Bd0149 FALSE 0.102 95 0
 1762417 1762418 Bd0149 Bd0150 TRUE 0.572 9 0
 1762419 1762420 Bd0152 Bd0153 TRUE 0.952 13 17.359
 1762420 1762421 Bd0153 Bd0154 TRUE 0.979 -3 28.224
 1762421 1762422 Bd0154 Bd0155 FALSE 0.263 36 0
 1762422 1762423 Bd0155 Bd0156 nifA FALSE 0.06 201 0
 1762423 1762424 Bd0156 Bd0157 nifA FALSE 0.204 77 0
 1762424 1762425 Bd0157 Bd0158 ygaD FALSE 0.373 21 -0.021
 1762425 1762426 Bd0158 Bd0159 ygaD uvrA TRUE 0.838 12 -15.086
 1762426 1762427 Bd0159 Bd0160 uvrA mrcA TRUE 0.898 -3 -8.297
 1762427 1762428 Bd0160 Bd0161 mrcA FALSE 0.184 61 0
 1762428 1762429 Bd0161 Bd0162 mscL FALSE 0.079 112 0
 1762429 1762430 Bd0162 Bd0163 mscL ydiY TRUE 0.797 16 -1.19
 1762431 1762432 Bd0164 Bd0165 ftsE FALSE 0.154 73 0
 1762432 1762433 Bd0165 Bd0166 ftsE ftsX TRUE 0.89 138 373.938
 1762433 1762434 Bd0166 Bd0168 ftsX nlpD TRUE 0.991 3 42.396
 1762434 1762435 Bd0168 Bd0169 nlpD ctpA TRUE 0.988 5 295.999
 1762435 1762436 Bd0169 Bd0170 ctpA FALSE 0.175 64 0
 1762437 1762438 Bd0172 Bd0173 FALSE 0.069 127 0
 1762439 1762440 Bd0175 Bd0176 trx TRUE 0.592 5 0
 1762441 1762442 Bd0177 Bd0178 ppiA glnE TRUE 0.738 36 -10.259
 1762442 1762443 Bd0178 Bd0179 glnE aglW TRUE 0.767 -7 -7.127
 1762443 1762444 Bd0179 Bd0180 aglW TRUE 0.964 14 39.019
 1762444 1762445 Bd0180 Bd0181 aglV TRUE 0.982 9 53.074
 1762445 1762446 Bd0181 Bd0182 aglV aglX TRUE 0.996 3 667.377
 1762446 1762447 Bd0182 Bd0183 aglX FALSE 0.184 61 0
 1762448 1762449 Bd0184 Bd0186 sufB TRUE 0.991 -7 110.447
 1762449 1762450 Bd0186 Bd0187 sufB sufC TRUE 0.98 43 823.348
 1762450 1762451 Bd0187 Bd0188 sufC sufD TRUE 0.995 10 835.614
 1762451 1762452 Bd0188 Bd0189 sufD csdB TRUE 0.99 6 672.919
 1762452 1762453 Bd0189 Bd0190 csdB NifU TRUE 0.976 -3 8.195
 1762453 1762454 Bd0190 Bd0191 NifU TRUE 0.584 7 0
 1762455 1762456 Bd0192 Bd0193 TRUE 0.61 -18 0
 1762456 1762457 Bd0193 Bd0194 FALSE 0.081 158 0
 1762458 1762459 Bd0197 Bd0198 xseA xseB TRUE 0.997 2 253.734
 1762459 1762460 Bd0198 Bd0199 xseB yqiD TRUE 0.99 4 685.538
 1762460 1762461 Bd0199 Bd0200 yqiD TRUE 0.987 2 100.116
 1762461 1762462 Bd0200 Bd0201 TRUE 0.613 11 -1.011
 1762462 1762463 Bd0201 Bd0202 pepP TRUE 0.666 9 -1.26
 1762467 1762468 Bd0206 Bd0208 glpD TRUE 0.598 4 0
 1762470 1762471 Bd0210 Bd0211 mreB FALSE 0.204 55 0
 1762471 1762472 Bd0211 Bd0213 mreB FALSE 0.236 60 0
 1762472 1762473 Bd0213 Bd0214 FALSE 0.159 71 0
 1762473 1762474 Bd0214 Bd0216 TRUE 0.621 -3 0
 1762474 1762475 Bd0216 Bd0217 FALSE 0.061 158 0
 1762477 1762478 Bd0220 Bd0221 TRUE 0.984 1 184.501
 1762478 1762479 Bd0221 Bd0222 FALSE 0.06 169 0
 1762481 1762482 Bd0224 Bd0225 FALSE 0.087 106 0
 1762484 1762485 Bd0227 Bd0228 prkA FALSE 0.144 77 0
 1762485 1762486 Bd0228 Bd0229 prkA yhbH TRUE 0.989 0 704.595
 1762486 1762487 Bd0229 Bd0231 yhbH TRUE 0.977 13 488.283
 1762487 1762488 Bd0231 Bd0232 yciH TRUE 0.665 -3 -2.14
 1762488 1762489 Bd0232 Bd0233 yciH TRUE 0.511 19 0
 1762489 1762490 Bd0233 Bd0234 FALSE 0.236 60 0
 1762491 1762492 Bd0235 Bd0236 rhlE TRUE 0.644 51 0
 1762492 1762493 Bd0236 Bd0237 TRUE 0.757 0 0
 1762493 1762494 Bd0237 Bd0238 TRUE 0.644 9 0
 1762495 1762496 Bd0239 Bd0240 rpsU TRUE 0.859 93 578.087
 1762496 1762497 Bd0240 Bd0241 dnaG TRUE 0.961 15 78.485
 1762497 1762498 Bd0241 Bd0242 dnaG rpoD TRUE 0.972 15 117.052
 1762498 1762499 Bd0242 trna_0005 rpoD FALSE 0.064 144 0
 1762499 1762500 trna_0005 Bd0243 FALSE 0.061 293 0
 1762501 1762502 Bd0244 Bd0245 atoE FALSE 0.064 142 0
 1762502 1762503 Bd0245 Bd0246 atoE FALSE 0.076 116 0
 1762505 1762506 Bd0248 Bd0249 TRUE 0.604 3 0
 1762506 1762507 Bd0249 Bd0250 TRUE 0.612 1 0
 1762509 1762510 Bd0252 Bd0253 TRUE 0.989 -3 263.186
 1762510 1762511 Bd0253 Bd0254 uvrC FALSE 0.337 83 0
 1762511 1762512 Bd0254 Bd0255 uvrC TRUE 0.765 21 0
 1762515 1762516 Bd0258 Bd0259 prsA nhaC TRUE 0.688 3 -1.019
 1762516 1762517 Bd0259 Bd0260 nhaC FALSE 0.234 44 0
 1762517 1762518 Bd0260 Bd0262 tsr TRUE 0.553 10 0
 1762518 1762519 Bd0262 Bd0263 tsr FALSE 0.06 169 0
 1762522 1762523 Bd0266 Bd0267 gcvH glnA TRUE 0.547 75 -1.186
 1762523 1762524 Bd0267 Bd0268 glnA glnB TRUE 0.978 32 229.305
 1762525 1762526 Bd0269 Bd0271 cspR TRUE 0.615 -7 0
 1762526 1762527 Bd0271 Bd0272 cspR secA FALSE 0.165 131 -37.008
 1762527 1762528 Bd0272 Bd0273 secA TRUE 0.612 1 0
 1762528 1762529 Bd0273 Bd0274 TRUE 0.609 -19 0
 1762529 1762530 Bd0274 Bd0275 FALSE 0.114 87 0
 1762531 1762532 Bd0276 Bd0277 TRUE 0.608 2 0
 1762532 1762533 Bd0277 Bd0278 FALSE 0.166 67 0
 1762533