VIMSS Operon Predictions for Bradyrhizobium japonicum

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
 315212 315213 blr0001 blr0002 FALSE 0.222 56 0
 315213 315214 blr0002 blr0003 FALSE 0.002 2066 0
 315214 315215 blr0003 bsr0004 FALSE 0.005 557 0
 315216 315217 bll0005 bll0006 nrdB FALSE 0.06 222 0
 315217 315218 bll0006 bll0007 nrdB TRUE 0.999 -18 305.32
 315218 315219 bll0007 bll0008 FALSE 0.103 173 0
 315219 315220 bll0008 bll0009 FALSE 0.03 274 0
 315220 315221 bll0009 bll0010 FALSE 0.004 631 0
 315221 315222 bll0010 bll0011 FALSE 0.136 129 0
 315223 315224 blr0012 blr0013 FALSE 0.017 327 0
 315225 315226 bll0014 bll0015 FALSE 0.253 -124 0
 315226 315227 bll0015 bsl0016 TRUE 0.954 -3 0
 315228 315229 blr0017 blr0018 TRUE 0.996 -3 0
 315229 315230 blr0018 blr0019 FALSE 0.019 321 0
 315231 315232 bll0020 bll0021 FALSE 0.332 126 0.846
 315233 315234 bsr0022 blr0023 FALSE 0.121 157 0
 315234 315235 blr0023 blr0024 FALSE 0.005 553 0
 315236 315237 bll0025 bll0026 FALSE 0.266 46 -1.352
 315238 315239 bsr0027 blr0028 FALSE 0.005 515 0
 315239 315240 blr0028 bsr0029 FALSE 0.159 97 0
 315240 315241 bsr0029 blr0030 FALSE 0.164 93 0
 315242 315243 bll0031 bsl0032 FALSE 0.261 44 0
 315244 315245 bsr0033 blr0034 FALSE 0.01 413 0
 315245 315246 blr0034 blr0035 TRUE 0.843 -3 -0.446
 315246 315247 blr0035 bsr0036 FALSE 0.145 119 0
 315247 315248 bsr0036 blr0037 TRUE 0.638 13 0
 315248 315249 blr0037 bsr0038 FALSE 0.043 258 0
 315249 315250 bsr0038 bsr0039 FALSE 0.01 399 0
 315251 315252 bll0040 bsl0041 FALSE 0.149 109 0
 315252 315253 bsl0041 bll0042 FALSE 0.008 425 0
 315253 315254 bll0042 bll0043 traG TRUE 0.988 8 51.381
 315254 315255 bll0043 bll0044 traG TRUE 0.999 -3 8.046
 315255 315256 bll0044 bll0045 FALSE 0.095 334 5.395
 315256 315257 bll0045 bll0046 TRUE 0.984 5 7.773
 315257 315258 bll0046 bll0047 traF TRUE 0.782 35 8.677
 315258 315259 bll0047 bll0048 traF TRUE 0.997 -3 35.825
 315259 315260 bll0048 bsl0049 TRUE 0.976 -13 27.618
 315260 315261 bsl0049 bll0050 TRUE 0.997 -3 34.659
 315261 315262 bll0050 bll0051 repA TRUE 0.982 -3 0.045
 315262 315263 bll0051 bll0052 repA FALSE 0.24 -148 0
 315263 315264 bll0052 bll0053 FALSE 0.171 84 0
 315264 315265 bll0053 bsl0054 FALSE 0.076 211 3.047
 315266 315267 bsr0055 blr0056 FALSE 0.113 164 0
 315274 315275 bll0063 bll0064 FALSE 0.032 327 5.35
 315275 315276 bll0064 bll0065 FALSE 0.219 57 0
 315276 315277 bll0065 bll0066 FALSE 0.091 128 0.547
 315279 315280 bll0068 bll0069 TRUE 0.925 8 0.225
 315280 315281 bll0069 bll0070 TRUE 0.991 -3 2.984
 315282 315283 bsr0071 blr0072 FALSE 0.1 76 -2.485
 315283 315284 blr0072 blr0073 TRUE 0.992 1 9.22
 315284 315285 blr0073 blr0074 TRUE 0.942 -16 2.427
 315286 315287 bll0075 bll0076 FALSE 0.146 116 0
 315288 315289 blr0077 bsr0078 FALSE 0.048 250 0
 315292 315293 bll0081 bll0082 FALSE 0.164 92 0
 315293 315294 bll0082 bll0083 FALSE 0.111 166 0
 315296 315297 bll0085 bll0086 FALSE 0.301 128 5.772
 315297 315298 bll0086 bll0087 FALSE 0.145 119 0
 315298 315299 bll0087 bll0088 TRUE 0.986 0 1.243
 315299 315300 bll0088 bll0089 TRUE 0.974 0 -0.175
 315300 315301 bll0089 bll0090 TRUE 1 -3 67.475
 315301 315302 bll0090 bll0091 TRUE 0.996 11 33.517
 315303 315304 blr0092 bsr0093 FALSE 0.413 128 1.044
 315304 315305 bsr0093 blr0094 FALSE 0.202 64 0
 315305 315306 blr0094 blr0095 FALSE 0.016 339 0
 315309 315310 bsl0098 bll0099 glt FALSE 0.09 103 -7.312
 315310 315311 bll0099 bll0100 glt FALSE 0.003 491 -3.467
 315313 315314 bll0102 bll0104 gltI gltP TRUE 0.848 10 11.839
 315315 315316 blr0103 blr0105 FALSE 0.037 261 0
 315316 315317 blr0105 blr0106 FALSE 0.005 548 0
 315317 315318 blr0106 blr0107 TRUE 0.991 -3 1.627
 315319 315320 bll0108 bll0109 TRUE 0.772 -34 -0.527
 315322 315323 bll0111 bll0112 TRUE 0.984 -28 10.004
 315323 315324 bll0112 bll0113 TRUE 0.859 112 10.004
 315324 315325 bll0113 bll0114 FALSE 0.184 44 -0.827
 315330 315331 blr0119 blr0120 TRUE 0.566 -45 0
 315333 315334 blr0122 blr0123 TRUE 0.738 -45 0.251
 315334 315335 blr0123 blr0124 TRUE 0.949 -7 0.251
 315336 402927 bll0125 Bjat01 tRNA-Arg FALSE 0.135 130 0
 315337 315338 blr0126 bsr0127 FALSE 0.13 125 -0.068
 315339 315340 bll0128 bll0129 FALSE 0.249 47 0
 315340 315341 bll0129 bll0130 FALSE 0.352 29 0
 315341 315342 bll0130 bll0131 FALSE 0.313 -63 0
 315342 315343 bll0131 bll0132 FALSE 0.159 97 0
 315343 315344 bll0132 bll0133 FALSE 0.116 161 0
 315344 315345 bll0133 bll0134 FALSE 0.03 275 0
 315346 315347 blr0135 bsr0136 TRUE 0.644 48 1.953
 315349 315350 blr0138 blr0139 TRUE 0.99 17 65.078
 315350 315351 blr0139 blr0140 TRUE 0.956 18 0.778
 315352 315353 bll0141 bll0142 FALSE 0.046 240 0
 315353 315354 bll0142 bll0143 TRUE 0.989 -3 1.089
 315354 315355 bll0143 bll0144 FALSE 0.366 155 0.851
 315356 315357 blr0145 blr0146 FALSE 0.416 26 0
 315357 315358 blr0146 blr0147 blr0147 FALSE 0.217 -922 0
 315360 315361 blr0149 blr0150 cyoA cyoB TRUE 0.997 12 141.646
 315361 315362 blr0150 blr0151 cyoB cyoC TRUE 1 1 482.251
 315362 315363 blr0151 blr0152 cyoC cyoD TRUE 1 -3 430.294
 315363 315364 blr0152 blr0153 cyoD TRUE 0.997 -3 25.621
 315364 315365 blr0153 blr0154 TRUE 0.872 -55 13.458
 315365 315366 blr0154 blr0155 TRUE 0.998 -10 120.806
 315367 315368 bll0156 bll0157 FALSE 0.191 147 6.382
 315368 315369 bll0157 bsl0158 TRUE 0.597 133 9.518
 315369 315370 bsl0158 bll0159 mgpS TRUE 0.699 49 7.084
 315370 315371 bll0159 bsl0160 mgpS FALSE 0.012 371 0
 315371 315372 bsl0160 bll0161 FALSE 0.063 219 0
 315375 315376 blr0164 blr0165 FALSE 0.125 153 0
 315376 315377 blr0165 blr0166 ftsZ FALSE 0.187 90 0
 315378 315379 bll0167 bsl0168 FALSE 0.091 185 0
 315379 315380 bsl0168 bsl0169 FALSE 0.026 286 0
 315380 315381 bsl0169 bsl0170 TRUE 0.846 -7 0
 315382 315383 blr0171 blr0172 FALSE 0.212 60 0
 315383 315384 blr0172 bsr0173 FALSE 0.097 180 0
 315385 315386 bll0174 bll0175 FALSE 0.06 170 -5.755
 315386 315387 bll0175 bll0176 FALSE 0.126 151 0
 315387 315388 bll0176 bll0177 FALSE 0.261 44 0
 315388 315389 bll0177 bll0178 cobT TRUE 0.996 -3 14.116
 315389 315390 bll0178 bll0179 cobT TRUE 0.929 -3 -1.422
 315390 315391 bll0179 bll0180 cobS TRUE 0.838 4 -1.422
 315397 315398 bll0186 bll0187 aroB FALSE 0.475 93 -5.541
 315398 315399 bll0187 bll0188 aroB TRUE 0.999 -3 39.348
 315400 315401 bsr0189 blr0190 xerD TRUE 0.881 18 5.084
 315401 315402 blr0190 blr0191 xerD accA FALSE 0.462 182 4.639
 315402 315403 blr0191 blr0192 accA FALSE 0.008 411 8.987
 315404 315405 bll0193 bll0194 TRUE 0.966 -7 2.818
 315405 315406 bll0194 bll0195 TRUE 0.781 -52 2.818
 315406 315407 bll0195 bll0196 TRUE 0.988 7 4.015
 315407 315408 bll0196 bll0197 TRUE 0.994 5 4.245
 315408 315409 bll0197 bll0198 TRUE 0.549 37 0.169
 315409 315410 bll0198 bll0199 FALSE 0.22 165 -0.011
 315412 315413 bsl0201 bll0202 TRUE 0.909 3 0
 315413 315414 bll0202 bll0203 TRUE 0.867 5 0
 315414 315415 bll0203 bll0204 secA FALSE 0.012 393 0
 315416 315417 blr0205 blr0206 argJ TRUE 0.754 103 31.971
 315417 315418 blr0206 blr0207 argJ TRUE 0.994 6 132.487
 315420 315421 blr0209 bsr0210 comF TRUE 0.927 48 40.355
 315421 315422 bsr0210 blr0211 TRUE 0.999 -3 37.281
 315422 315423 blr0211 blr0212 TRUE 0.997 -3 21.692
 315424 315425 bll0213 bll0214 ubiG FALSE 0.016 279 -8.048
 315425 315426 bll0214 bll0215 ubiG TRUE 0.669 21 -0.171
 315427 315428 blr0216 blr0217 lysC ptsP FALSE 0.309 289 29.334
 315428 315429 blr0217 blr0218 ptsP prfA TRUE 0.599 59 -3.73
 315429 315430 blr0218 blr0219 prfA hemK TRUE 1 -3 974.54
 315430 315431 blr0219 blr0220 hemK FALSE 0.018 464 29.689
 315433 315434 blr0222 blr0223 gloB TRUE 0.848 24 11.683
 315435 315436 bll0224 bll0225 phbB FALSE 0.228 169 -0.321
 315436 315437 bll0225 bll0226 phbB atoB FALSE 0.484 251 35.778
 315438 315439 blr0227 blr0228 FALSE 0.103 74 -1.471
 315444 315445 bll0233 bll0234 FALSE 0.439 68 0
 315445 315446 bll0234 bll0235 TRUE 0.994 -3 6.533
 315446 315447 bll0235 bll0236 FALSE 0.234 27 -0.377
 315448 315449 blr0237 blr0238 TRUE 0.993 -3 27.51
 315449 315450 blr0238 blr0239 FALSE 0.35 -31 -0.481
 315453 315454 bll0242 bll0243 recQ FALSE 0.089 89 -3.459
 315454 315455 bll0243 bll0244 TRUE 0.671 -22 0
 315455 315456 bll0244 bll0245 cysD TRUE 0.977 13 3.611
 315456 315457 bll0245 bll0246 cysD bam FALSE 0.017 327 0
 315458 315459 bsr0247 blr0248 FALSE 0.15 108 0
 315459 315460 blr0248 blr0249 TRUE 0.954 -3 0
 315461 315462 bll0250 bll0251 mocA TRUE 0.871 11 6.08
 315463 315464 blr0252 blr0253 FALSE 0.065 160 -4.654
 315465 315466 bll0254 bsl0255 FALSE 0.096 181 0
 315466 315467 bsl0255 bll0256 TRUE 0.954 -3 0
 315468 315469 blr0257 blr0258 TRUE 0.996 -3 -1.389
 315469 315470 blr0258 blr0259 TRUE 0.752 94 1.879
 315470 315471 blr0259 blr0260 FALSE 0.124 154 0
 315471 315472 blr0260 blr0261 FALSE 0.067 212 0
 315472 315473 blr0261 blr0262 FALSE 0.048 237 0
 315474 315475 bll0263 bll0264 mdcF TRUE 0.756 10 -0.073
 315475 315476 bll0264 bll0265 mdcF mdcB TRUE 0.93 -3 -0.642
 315476 315477 bll0265 bll0266 mdcB mdcG TRUE 0.99 -3 23.352
 315477 315478 bll0266 bll0267 mdcG mdcE TRUE 0.949 -25 10.546
 315478 315479 bll0267 bll0268 mdcE mdcD TRUE 0.857 -13 5.93
 315479 315480 bll0268 bll0269 mdcD mdcC FALSE 0.333 72 51.102
 315480 315481 bll0269 bll0270 mdcC mdcA TRUE 0.969 11 107.133
 315481 315482 bll0270 bll0271 mdcA TRUE 0.916 -3 -0.11
 315482 315483 bll0271 bll0272 FALSE 0.158 98 0
 315483 315484 bll0272 bsl0273 TRUE 0.79 8 0
 315487 315488 blr0276 blr0277 TRUE 0.996 -3 9.539
 315488 315489 blr0277 blr0278 TRUE 0.747 -13 -0.164
 315489 315490 blr0278 blr0279 FALSE 0.153 103 0
 315493 315494 bll0282 bll0283 TRUE 1 3 477.85
 315494 315495 bll0283 bll0284 mqo TRUE 0.569 20 -2.877
 315495 315496 bll0284 bll0285 mqo TRUE 0.761 43 6.408
 315496 315497 bll0285 bll0286 fumC FALSE 0.27 74 2.168
 315497 315498 bll0286 bll0287 fumC FALSE 0.235 -60 -0.079
 315498 315499 bll0287 bll0288 FALSE 0.458 19 -0.303
 315499 315500 bll0288 bll0289 TRUE 0.805 4 -0.612
 315500 315501 bll0289 bll0290 FALSE 0.015 344 0
 315501 315502 bll0290 bll0291