VIMSS Operon Predictions for Bordetella parapertussis 12822

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
 506828 506829 BPP0001 BPP0002 gidA gidB TRUE 0.993 -3 540.738
 506829 506830 BPP0002 BPP0003 gidB parA TRUE 0.991 -3 413.363
 506830 506831 BPP0003 BPP0004 parA TRUE 0.741 7 -2.659
 506831 506832 BPP0004 BPP0005 parB FALSE 0.268 44 -2.27
 506832 506833 BPP0005 BPP0006 parB ansB FALSE 0.347 -7 -23.953
 506833 506834 BPP0006 BPPt01 ansB FALSE 0.137 110 0
 506834 506835 BPPt01 BPPt02 FALSE 0.05 189 0
 506835 506836 BPPt02 BPPt03 TRUE 0.735 7 0
 506836 506837 BPPt03 BPP0007 tufA FALSE 0.215 57 0
 506837 506838 BPP0007 BPPt04 tufA FALSE 0.136 111 0
 506838 506839 BPPt04 BPP0008 secE FALSE 0.231 53 0
 506839 506840 BPP0008 BPP0009 secE nusG TRUE 0.986 10 221.122
 506840 506841 BPP0009 BPP0010 nusG rplK TRUE 0.949 64 1160.621
 506841 506842 BPP0010 BPP0011 rplK rplA TRUE 0.999 3 1523.829
 506842 506843 BPP0011 BPP0012 rplA rplJ TRUE 0.902 243 1137.006
 506843 506844 BPP0012 BPP0013 rplJ rplL TRUE 0.986 82 1517.844
 506844 506845 BPP0013 BPP0014 rplL rpoB TRUE 0.698 136 813.631
 506845 506846 BPP0014 BPP0015 rpoB rpoC TRUE 0.998 0 814.747
 506849 506850 BPP0018 BPP0019 TRUE 0.751 2 0
 506850 506851 BPP0019 BPP0020 TRUE 0.905 18 36.943
 506853 506854 BPP0022 BPP0023 TRUE 0.98 6 74.331
 506855 506856 BPP0024 BPP0025 rpsL rpsG TRUE 0.973 164 1490.385
 506856 506857 BPP0025 BPP0026 rpsG fusA TRUE 0.995 18 899.75
 506857 506858 BPP0026 BPP0027 fusA tuf TRUE 0.983 77 414.846
 506858 506859 BPP0027 BPP0028 tuf rpsJ TRUE 0.971 64 542.502
 506859 506860 BPP0028 BPP0029 rpsJ rplC TRUE 0.861 340 1252.328
 506860 506861 BPP0029 BPP0030 rplC rplD TRUE 0.999 5 1400.776
 506861 506862 BPP0030 BPP0031 rplD rplW TRUE 0.998 -3 1393.267
 506862 506863 BPP0031 BPP0032 rplW rplB TRUE 0.999 1 1411.061
 506863 506864 BPP0032 BPP0033 rplB rpsS TRUE 0.999 13 1457.925
 506864 506865 BPP0033 BPP0034 rpsS rplV TRUE 0.999 4 1298.281
 506865 506866 BPP0034 BPP0035 rplV rpsC TRUE 0.999 10 1318.519
 506866 506867 BPP0035 BPP0036 rpsC rplP TRUE 0.999 3 1518.915
 506867 506868 BPP0036 BPP0037 rplP rpmC TRUE 0.999 11 1150.681
 506868 506869 BPP0037 BPP0038 rpmC rpsQ TRUE 0.999 2 1143.168
 506870 506871 BPP0039 BPP0040 FALSE 0.151 87 0
 506872 506873 BPP0041 BPP0042 rplN rplX TRUE 0.999 11 1368.826
 506873 506874 BPP0042 BPP0043 rplX rplE TRUE 0.999 13 1385.841
 506874 506875 BPP0043 BPP0044 rplE rpsN TRUE 0.998 13 694.193
 506875 506876 BPP0044 BPP0045 rpsN rpsH TRUE 0.998 11 692.107
 506876 506877 BPP0045 BPP0046 rpsH rplF TRUE 0.999 11 1620.216
 506877 506878 BPP0046 BPP0047 rplF rplR TRUE 0.997 22 1555.236
 506878 506879 BPP0047 BPP0048 rplR rpsE TRUE 0.998 16 1427.542
 506879 506880 BPP0048 BPP0049 rpsE rpmD TRUE 0.999 4 1097.176
 506880 506881 BPP0049 BPP0050 rpmD rplO TRUE 0.999 10 1178.927
 506881 506882 BPP0050 BPP0051 rplO secY TRUE 0.993 15 1451.777
 506882 506883 BPP0051 BPP0052 secY infA TRUE 0.993 10 383.032
 506883 506884 BPP0052 BPP0053 infA rpmJ TRUE 0.962 35 572.412
 506884 506885 BPP0053 BPP0054 rpmJ rpsM TRUE 0.978 42 878.795
 506885 506886 BPP0054 BPP0055 rpsM rpsK TRUE 0.998 16 1582.568
 506886 506887 BPP0055 BPP0056 rpsK rpsD TRUE 0.999 12 811.405
 506887 506888 BPP0056 BPP0057 rpsD rpoA TRUE 0.786 215 808.944
 506888 506889 BPP0057 BPP0058 rpoA TRUE 0.881 159 1389.67
 506891 506892 BPP0060 BPP0061 cutA TRUE 0.973 11 195.505
 506892 506893 BPP0061 BPP0062 FALSE 0.346 41 -2.635
 506894 506895 BPP0063 BPP0064 hemB TRUE 0.945 -3 15.66
 506896 506897 BPP0065 BPP0066 TRUE 0.626 118 65.588
 506897 506898 BPP0066 BPP0067 TRUE 0.991 10 72.388
 506902 506903 BPP0071 BPP0072 aroK aroB TRUE 0.998 0 572.531
 506903 506904 BPP0072 BPP0073 aroB TRUE 0.962 -3 55.324
 506905 506906 BPP0074 BPP0075 uvrA FALSE 0.219 56 0
 506907 506908 BPP0076 BPP0077 ssb FALSE 0.411 233 106.594
 506910 506911 BPP0079 BPP0080 bfrC FALSE 0.066 137 -1.004
 506911 506912 BPP0080 BPP0081 TRUE 0.552 19 0.006
 506912 506913 BPP0081 BPP0082 FALSE 0.408 29 0.006
 506913 506914 BPP0082 BPP0083 FALSE 0.408 54 0.049
 506916 506917 BPP0085 BPP0086 FALSE 0.485 39 0.049
 506917 506918 BPP0086 BPP0087 FALSE 0.157 153 0.049
 506918 506919 BPP0087 BPP0088 TRUE 0.879 7 -0.013
 506919 506920 BPP0088 BPP0089 FALSE 0.124 160 0.049
 506920 506921 BPP0089 BPP0090 FALSE 0.256 26 -0.72
 506921 506922 BPP0090 BPP0091 TRUE 0.851 64 84.967
 506922 506923 BPP0091 BPP0092 TRUE 0.987 -12 36.04
 506923 506924 BPP0092 BPP0093 TRUE 0.603 28 0.652
 506925 506926 BPP0094 BPP0095 TRUE 0.767 9 0.006
 506926 506927 BPP0095 BPP0096 glcB FALSE 0.192 36 -3.099
 506929 506930 BPP0098 BPP0099 FALSE 0.022 226 -1.057
 506930 506931 BPP0099 BPP0100 FALSE 0.015 266 -1.415
 506931 506932 BPP0100 BPP0101 FALSE 0.304 87 -18.44
 506933 506934 BPP0102 BPP0103 FALSE 0.006 288 -4.389
 506934 506935 BPP0103 BPP0104 FALSE 0.017 348 0
 506935 506936 BPP0104 BPP0105 FALSE 0.063 167 0
 506936 506937 BPP0105 BPP0106 TRUE 0.955 -16 2.661
 506937 506938 BPP0106 BPP0107 TRUE 0.84 36 2.661
 506938 506939 BPP0107 BPP0108 TRUE 0.916 -3 6.739
 506940 506941 BPP0109 BPP0110 TRUE 0.819 -3 1.605
 506942 506943 BPP0111 BPP0112 FALSE 0.062 127 -1.781
 506943 506944 BPP0112 BPP0113 FALSE 0.027 194 -3.286
 506944 506945 BPP0113 BPP0114 TRUE 0.965 1 61.506
 506945 506946 BPP0114 BPP0115 aspS TRUE 0.885 41 72.846
 506946 506947 BPP0115 BPP0116 aspS FALSE 0.045 113 -5.715
 506947 506948 BPP0116 BPP0117 TRUE 0.831 -54 5.892
 506949 506950 BPP0118 BPP0119 TRUE 0.555 16 0
 506950 506951 BPP0119 BPP0120 FALSE 0.237 51 0
 506952 506953 BPP0121 BPP0122 TRUE 0.99 -3 46.057
 506953 506954 BPP0122 BPP0123 FALSE 0.446 121 10.471
 506954 506955 BPP0123 BPP0124 wbmU FALSE 0.239 133 4.268
 506955 506956 BPP0124 BPP0125 wbmU wbmT TRUE 0.677 -3 0
 506956 506957 BPP0125 BPP0126 wbmT wbmS TRUE 0.677 -3 0
 506957 506958 BPP0126 BPP0127 wbmS wbmR TRUE 0.733 -3 0.006
 506958 506959 BPP0127 BPP0128 wbmR wbmQ TRUE 0.82 23 0
 506959 506960 BPP0128 BPP0129 wbmQ wbmP TRUE 0.677 -3 0
 506960 506961 BPP0129 BPP0130 wbmP wbmO TRUE 0.727 8 0
 506961 506962 BPP0130 BPP0131 wbmO wbmN TRUE 0.733 -3 0.006
 506962 506963 BPP0131 BPP0132 wbmN wbmM TRUE 0.958 -7 0.006
 506963 506964 BPP0132 BPP0133 wbmM wbmL TRUE 0.987 7 8.045
 506964 506965 BPP0133 BPP0134 wbmL wbmK TRUE 0.733 -3 0.006
 506965 506966 BPP0134 BPP0135 wbmK wbmJ FALSE 0.269 56 0.006
 506966 506967 BPP0135 BPP0136 wbmJ wbmI FALSE 0.185 101 0.006
 506967 506968 BPP0136 BPP0137 wbmI wbmH FALSE 0.415 29 0.006
 506968 506969 BPP0137 BPP0138 wbmH wbmG TRUE 0.983 5 0.006
 506969 506970 BPP0138 BPP0139 wbmG wbmF TRUE 0.98 5 -0.512
 506971 506972 BPP0140 BPP0141 wbmE wbmD FALSE 0.145 123 0.006
 506972 506973 BPP0141 BPP0142 wbmD wbmC FALSE 0.208 76 0.006
 506974 506975 BPP0143 BPP0144 wbmB wbmA TRUE 0.922 -10 0.006
 506976 506977 BPP0145 BPP0146 bplL bplJ FALSE 0.3 49 0.006
 506977 506978 BPP0146 BPP0147 bplJ bplI FALSE 0.295 50 0.006
 506978 506979 BPP0147 BPP0148 bplI bplH TRUE 0.619 -3 -0.492
 506979 506980 BPP0148 BPP0149 bplH bplG FALSE 0.206 262 -1.678
 506980 506981 BPP0149 BPP0150 bplG bplF TRUE 0.991 -3 50.709
 506981 506982 BPP0150 BPP0151 bplF bplE TRUE 0.889 18 -1.642
 506982 506983 BPP0151 BPP0152 bplE bplD TRUE 0.882 24 23.869
 506983 506984 BPP0152 BPP0153 bplD bplC TRUE 0.866 110 2.359
 506984 506985 BPP0153 BPP0154 bplC bplB TRUE 0.987 4 64.801
 506985 506986 BPP0154 BPP0155 bplB bplA TRUE 0.965 4 14.73
 506987 506988 BPP0156 BPP0157 rfaC kdtA TRUE 0.987 2 84.708
 506989 506990 BPP0158 BPP0159 baf FALSE 0.061 171 0
 506990 506991 BPP0159 BPP0160 baf birA TRUE 0.677 -3 0
 506992 506993 BPP0161 BPP0162 TRUE 0.996 0 248.763
 506993 506994 BPP0162 BPP0163 TRUE 0.995 -13 242.783
 506994 506995 BPP0163 BPP0164 TRUE 0.985 1 89.164
 506995 506996 BPP0164 BPP0165 FALSE 0.105 30 -20.087
 506996 506997 BPP0165 BPP0166 FALSE 0.304 133 36.295
 506997 506998 BPP0166 BPP0167 TRUE 0.977 3 57.898
 506998 506999 BPP0167 BPP0168 TRUE 0.699 76 58.814
 506999 507000 BPP0168 BPP0169 lipB TRUE 0.963 8 213.24
 507000 507001 BPP0169 BPP0170 lipB lipA TRUE 0.99 62 356.083
 507002 507003 BPP0171 BPP0172 rfbC rfbD TRUE 0.973 58 421.414
 507003 507004 BPP0172 BPP0173 rfbD rfbB TRUE 0.998 -63 494.994
 507004 507005 BPP0173 BPP0174 rfbB FALSE 0.341 36 -30.542
 507007 507008 BPP0176 BPP0177 hslU hslV TRUE 0.994 22 946.851
 507008 507009 BPP0177 BPP0178 hslV dksA FALSE 0.253 148 8.297
 507009 507010 BPP0178 BPP0179 dksA FALSE 0.07 144 27.501
 507010 507011 BPP0179 BPP0180 FALSE 0.06 277 -5.184
 507012 507013 BPP0181 BPP0182 TRUE 0.996 -3 581.712
 507013 507014 BPP0182 BPP0183 TRUE 0.993 -3 752.767
 507014 507015 BPP0183 BPP0184 FALSE 0.485 48 -1.19
 507015 507016 BPP0184 BPP0185 TRUE 0.919 -9 94.444
 507016 507017 BPP0185 BPP0186 FALSE 0.246 49 -1.38
 507018 507019 BPP0187 BPP0188 TRUE 0.971 15 298.481
 507019 507020 BPP0188 BPP0189 dapF TRUE 0.92 27 281.481
 507020 507021 BPP0189 BPP0190 dapF TRUE 0.699 43 12.831
 507021 507022 BPP0190 BPP0191 TRUE 0.992 -3 15.113
 507023 507024 BPP0192 BPP0193 metK FALSE 0.082 111 -1.524
 507024 507025 BPP0193 BPP0194 FALSE 0.098 80 -1.524
 507025 507026 BPP0194 BPP0195 acyH FALSE 0.008 280 -21.815
 507026 507027 BPP0195 BPP0196 acyH TRUE 0.553 71 40.957
 507027 507028 BPP0196 BPP0197 TRUE 0.945 0 43.008
 507029 507030 BPP0198 BPP0199 FALSE 0.157 64 -8.552
 507030 507031 BPP0199 BPP0200 TRUE 0.596 2 -11.119
 507031 507032 BPP0200 BPP0201 FALSE 0.014 277 -16.571
 507033 507034 BPP0202 BPP0203 cca TRUE 0.776 -3 -18.231
 507035 507036 BPP0204 BPP0205 FALSE 0.195 20 -12.371
 507036 507037 BPP0205 BPP0206 ung FALSE 0.254 167 -10.979
 507037 507038 BPP0206 BPP0207 ung FALSE 0.372 37 -20.508
 507038 507039 BPP0207 BPP0208 FALSE 0.134 53 -18.49
 507042 507043 BPP0211 BPP0212 fur TRUE 0.733 -3 0.006
 507045 507046 BPP0214 BPP0215 TRUE 0.699 -16 0.006
 507047 507048 BPP0216 BPP0217 TRUE 0.594 -3 -1.373
 507048 507049 BPP0217 BPP0218 FALSE 0.351 33 -3.136
 507049 507050 BPP0218 BPP0219 TRUE 0.727 14 -4.68
 507051 507052 BPP0220 BPP0221 TRUE 0.966 -3 100.945
 507052 507053 BPP0221 BPP0222 TRUE 0.751 2 0
 507054 507055 BPP0223 BPP0224 TRUE 0.773 69 102.551
 507055 507056 BPP0224 BPP0225 FALSE 0.196 62 0
 507056 507057 BPP0225 BPP0226 FALSE 0.132 113 0
 507057 507058 BPP0226 BPP0227 TRUE 0.989 11 100.772
 507058 507059 BPP0227 BPP0228 TRUE 0.989 11 97.328
 507059 507060 BPP0228 BPP0229 TRUE 0.987 4 149.885
 507063 507064 BPP0232 BPP0233 FALSE 0.073 96 -7.325
 507065 507066 BPP0234 BPP0235 FALSE 0.053 158 -0.354
 507067 507068 BPP0236 BPP0237 FALSE 0.47 114 -0.293
 507069 507070 BPP0238 BPP0239 hmgcL FALSE 0.156 143 0.049
 507070 507071 BPP0239 BPP0240 hmgcL smf FALSE 0.046 114 -18.364
 507071 507072 BPP0240 BPP0241 smf lrp FALSE 0.064 101 -6.888
 507073 507074 BPP0242 BPP0243 def FALSE 0.049 102 -14.619
 507074 507075 BPP0243