Effective results for Bordetella petrii DSM 12804 (eggnog40)
Summary
Number of putative secreted proteins: 290
- Predicted by T4SEpre: 47
- Predicted by EffectiveELD: 24 eukaryotic-like domains, contained in 253 proteins (120 high, 133 medium Z-score)
Predicted protein secretion systems (parentheses indicate weak positive predictions lacking more than 50% of core proteins of a secretion system): Type IV, Type VI
Protein based results
Putative secreted proteins (weak evidence indicated by parentheses)
| Protein | EffectiveT3 | EffectiveCCBD | T4SEpre | EffectiveELD | Predotar |
|---|---|---|---|---|---|
| 340100.Bpet4718 | (PF13607) (PF13549) (PF13380) | (mitochondrial) | |||
| 340100.Bpet1210 | (PF13607) (PF13549) (PF13380) | (mitochondrial) | |||
| 340100.Bpet4827 | (PF13683) PF13276 | mitochondrial | |||
| 340100.Bpet0589 | (PF13607) (PF13549) | ER; (ER) | |||
| 340100.Bpet4633 | (PF13683) PF13276 | mitochondrial | |||
| 340100.Bpet3283 | (PF13607) (PF13549) (PF13380) | ||||
| 340100.Bpet3869 | + | ER | |||
| 340100.Bpet3678 | (PF01144) | (ER) | |||
| 340100.Bpet0392 | (PF02515) | mitochondrial; (mitochondrial) | |||
| 340100.Bpet1257 | + | ER | |||
| 340100.Bpet0651 | PF00665 PF13276 | (ER) | |||
| 340100.Bpet4595 | + | (ER) | |||
| 340100.Bpet2987 | (PF13607) (PF13549) (PF13380) | ||||
| 340100.Bpet2661 | (PF07678) | ER | |||
| 340100.Bpet4479 | PF00665 PF13276 | (ER) | |||
| 340100.Bpet3550 | (PF02515) | (ER) | |||
| 340100.Bpet0202 | PF00665 | (mitochondrial) | |||
| 340100.Bpet0601 | + | mitochondrial | |||
| 340100.Bpet3497 | + | ER | |||
| 340100.Bpet1410 | PF00665 PF13276 | (mitochondrial) | |||
| 340100.Bpet0786 | PF00665 PF13276 | (ER) | |||
| 340100.Bpet4099 | + | mitochondrial | |||
| 340100.Bpet3572 | (PF16155) | (mitochondrial) | |||
| 340100.Bpet3788 | (PF13607) (PF13549) (PF13380) | ||||
| 340100.Bpet1225 | + | ER | |||
| 340100.Bpet1221 | (PF02515) | (ER); ER | |||
| 340100.Bpet2028 | + | ER | |||
| 340100.Bpet3986 | PF00665 | (mitochondrial) | |||
| 340100.Bpet3438 | (PF02515) | (ER) | |||
| 340100.Bpet1215 | (PF13607) (PF13549) (PF13380) | ||||
| 340100.Bpet3531 | + | ER | |||
| 340100.Bpet0508 | PF00665 PF13276 | (ER) | |||
| 340100.Bpet1498 | (PF02899) | (mitochondrial); mitochondrial | |||
| 340100.Bpet0050 | (PF13607) (PF13549) (PF13380) | ||||
| 340100.Bpet1014 | PF00665 | (ER) | |||
| 340100.Bpet1245 | (PF02515) | (ER) | |||
| 340100.Bpet4700 | (PF07364) (PF07171) | ||||
| 340100.Bpet3288 | PF00665 PF13276 | ||||
| 340100.Bpet0808 | (PF07364) (PF07171) | ||||
| 340100.Bpet2093 | PF00665 PF13276 | ||||
| 340100.Bpet3292 | (PF02515) | (ER) | |||
| 340100.Bpet3938 | PF00665 PF13276 | ||||
| 340100.Bpet0225 | + | (plastid) | |||
| 340100.Bpet2526 | + | (plastid) | |||
| 340100.Bpet0216 | PF01527 | (mitochondrial) | |||
| 340100.Bpet0211 | PF00665 PF13276 | ||||
| 340100.Bpet0367 | (PF02515) | (mitochondrial) | |||
| 340100.Bpet4306 | + | (PF00436) | |||
| 340100.Bpet1452 | PF00665 PF13276 | ||||
| 340100.Bpet3552 | + | (mitochondrial) | |||
| 340100.Bpet0207 | (PF13683) PF13276 | ||||
| 340100.Bpet4044 | (PF07364) (PF07171) | ||||
| 340100.Bpet3015 | PF00665 PF13276 | ||||
| 340100.Bpet4319 | (PF02515) | (ER) | |||
| 340100.Bpet1155 | (PF02515) | (mitochondrial) | |||
| 340100.Bpet2835 | + | (ER) | |||
| 340100.Bpet1140 | PF01527 | (mitochondrial) | |||
| 340100.Bpet4292 | PF00665 PF13276 | ||||
| 340100.Bpet3780 | PF00665 PF13276 | ||||
| 340100.Bpet4242 | PF01527 | (mitochondrial) | |||
| 340100.Bpet1300 | PF00665 PF13276 | ||||
| 340100.Bpet1303 | (PF02899) | (mitochondrial) | |||
| 340100.Bpet1125 | PF00665 PF13276 | ||||
| 340100.Bpet3993 | PF00665 PF13276 | ||||
| 340100.Bpet1930 | PF00665 PF13276 | ||||
| 340100.Bpet3168 | PF00665 PF13276 | ||||
| 340100.Bpet3768 | PF00665 PF13276 | ||||
| 340100.Bpet1338 | PF00665 PF13276 | ||||
| 340100.Bpet1200 | PF01527 | (mitochondrial) | |||
| 340100.Bpet1204 | PF01527 | (mitochondrial) | |||
| 340100.Bpet1206 | PF01527 | (mitochondrial) | |||
| 340100.Bpet1115 | PF01527 | (mitochondrial) | |||
| 340100.Bpet1114 | PF01527 | (mitochondrial) | |||
| 340100.Bpet0523 | + | plastid | |||
| 340100.Bpet3987 | (PF13683) PF13276 | ||||
| 340100.Bpet1450 | (PF02899) | (mitochondrial) | |||
| 340100.Bpet4636 | (PF13683) PF13276 | ||||
| 340100.Bpet1108 | PF00665 PF13276 | ||||
| 340100.Bpet1105 | PF01527 | (mitochondrial) | |||
| 340100.Bpet0531 | + | (mitochondrial) | |||
| 340100.Bpet1463 | PF00665 PF13276 | ||||
| 340100.Bpet1917 | PF00665 PF13276 | ||||
| 340100.Bpet4039 | (PF07364) (PF07171) | ||||
| 340100.Bpet0195 | PF00665 PF13276 | ||||
| 340100.Bpet2438 | PF00665 PF13276 | ||||
| 340100.Bpet2119 | PF00665 PF13276 | ||||
| 340100.Bpet2112 | PF00665 PF13276 | ||||
| 340100.Bpet1495 | PF00665 PF13276 | ||||
| 340100.Bpet1653 | (PF03972) | (plastid) | |||
| 340100.Bpet0473 | + | plastid | |||
| 340100.Bpet1018 | PF00665 PF13276 | ||||
| 340100.Bpet2287 | (PF07287) | (plastid) | |||
| 340100.Bpet0607 | (PF13683) PF13276 | ||||
| 340100.Bpet0605 | PF01527 | (mitochondrial) | |||
| 340100.Bpet0863 | PF00665 PF13276 | ||||
| 340100.Bpet3721 | PF00665 PF13276 | ||||
| 340100.Bpet4815 | PF00665 PF13276 | ||||
| 340100.Bpet0281 | (PF07364) (PF07171) | ||||
| 340100.Bpet4600 | PF01527 | (mitochondrial) | |||
| 340100.Bpet3289 | PF01527 | ||||
| 340100.Bpet1038 | (PF00145) | ||||
| 340100.Bpet1039 | (PF02899) | ||||
| 340100.Bpet1036 | (PF00436) | ||||
| 340100.Bpet1037 | (PF01131) | ||||
| 340100.Bpet2639 | + | ||||
| 340100.Bpet1297 | (PF00436) | ||||
| 340100.Bpet0801 | (PF02515) | ||||
| 340100.Bpet3440 | + | ||||
| 340100.Bpet2094 | PF01527 | ||||
| 340100.Bpet4451 | (PF02515) | ||||
| 340100.Bpet3679 | (PF01144) | ||||
| 340100.Bpet3676 | (PF02515) | ||||
| 340100.Bpet0264 | (PF02515) | ||||
| 340100.Bpet1299 | PF01527 | ||||
| 340100.Bpet4716 | (PF03972) | ||||
| 340100.Bpet0485 | + | ||||
| 340100.Bpet0650 | + | ||||
| 340100.Bpet0652 | PF01527 | ||||
| 340100.Bpet3871 | (PF02615) | ||||
| 340100.Bpet2879 | (PF02515) | ||||
| 340100.Bpet1635 | (PF01144) | ||||
| 340100.Bpet1636 | (PF01144) | ||||
| 340100.Bpet0837 | (PF02515) | ||||
| 340100.Bpet3416 | + | ||||
| 340100.Bpet0341 | + | ||||
| 340100.Bpet4826 | PF01527 | ||||
| 340100.Bpet4585 | PF01527 | ||||
| 340100.Bpet4586 | PF00665 | ||||
| 340100.Bpet4213 | (PF00436) | ||||
| 340100.Bpet1298 | (PF01131) | ||||
| 340100.Bpet1453 | PF01527 | ||||
| 340100.Bpet1511 | + | ||||
| 340100.Bpet3591 | (PF01144) | ||||
| 340100.Bpet3590 | (PF01144) | ||||
| 340100.Bpet3939 | PF01527 | ||||
| 340100.Bpet2269 | (PF03972) | ||||
| 340100.Bpet3937 | (PF02615) | ||||
| 340100.Bpet0130 | (PF11969) | ||||
| 340100.Bpet1199 | PF00665 | ||||
| 340100.Bpet0221 | PF01527 | ||||
| 340100.Bpet0226 | (PF13683) | ||||
| 340100.Bpet0228 | PF01527 | not used | |||
| 340100.Bpet1175 | (PF04752) | ||||
| 340100.Bpet1174 | (PF01144) | ||||
| 340100.Bpet1173 | (PF01144) | ||||
| 340100.Bpet1616 | + | ||||
| 340100.Bpet0581 | + | ||||
| 340100.Bpet1500 | (PF02899) | ||||
| 340100.Bpet0034 | (PF01131) | ||||
| 340100.Bpet4905 | (PF00436) | ||||
| 340100.Bpet2680 | (PF02615) | ||||
| 340100.Bpet0215 | PF00665 | ||||
| 340100.Bpet0212 | PF01527 | ||||
| 340100.Bpet4478 | PF01527 | ||||
| 340100.Bpet4305 | (PF01131) | ||||
| 340100.Bpet1169 | + | ||||
| 340100.Bpet1406 | (PF13683) | ||||
| 340100.Bpet1405 | PF01527 | ||||
| 340100.Bpet0028 | (PF02515) | ||||
| 340100.Bpet1371 | (PF10014) | ||||
| 340100.Bpet0208 | PF01527 | ||||
| 340100.Bpet0201 | PF01527 | ||||
| 340100.Bpet3013 | PF01527 | ||||
| 340100.Bpet3014 | PF01527 | ||||
| 340100.Bpet0376 | (PF01144) | ||||
| 340100.Bpet0375 | (PF01144) | ||||
| 340100.Bpet3305 | (PF02515) | ||||
| 340100.Bpet1931 | PF01527 | ||||
| 340100.Bpet1790 | (PF01144) | ||||
| 340100.Bpet4634 | PF01527 | ||||
| 340100.Bpet1151 | (PF07287) | ||||
| 340100.Bpet1150 | PF01527 | ||||
| 340100.Bpet0767 | + | ||||
| 340100.Bpet3499 | (PF03972) | ||||
| 340100.Bpet1411 | PF01527 | ||||
| 340100.Bpet0947 | (PF00145) | ||||
| 340100.Bpet1960 | (PF02515) | ||||
| 340100.Bpet0785 | PF01527 | ||||
| 340100.Bpet2776 | + | ||||
| 340100.Bpet3790 | (PF02515) | ||||
| 340100.Bpet4786 | (PF02899) | ||||
| 340100.Bpet1094 | PF01527 | ||||
| 340100.Bpet3377 | + | ||||
| 340100.Bpet1789 | (PF01144) | ||||
| 340100.Bpet1147 | PF00665 | ||||
| 340100.Bpet1142 | PF01527 | ||||
| 340100.Bpet4529 | (PF01144) | ||||
| 340100.Bpet4528 | (PF01144) | ||||
| 340100.Bpet2785 | (PF02515) | ||||
| 340100.Bpet3781 | PF01527 | ||||
| 340100.Bpet1227 | (PF02515) | ||||
| 340100.Bpet1223 | (PF02515) | ||||
| 340100.Bpet1220 | (PF02515) | ||||
| 340100.Bpet4334 | PF01527 | ||||
| 340100.Bpet4335 | PF00665 | ||||
| 340100.Bpet0408 | (PF02615) | ||||
| 340100.Bpet1139 | PF00665 | ||||
| 340100.Bpet4241 | (PF13683) | ||||
| 340100.Bpet1042 | (PF00145) | ||||
| 340100.Bpet1041 | (PF02899) | ||||
| 340100.Bpet2966 | (PF02515) | ||||
| 340100.Bpet3563 | (PF02899) | ||||
| 340100.Bpet2158 | (PF02515) | ||||
| 340100.Bpet2483 | (PF02515) | ||||
| 340100.Bpet3771 | (PF00436) | ||||
| 340100.Bpet1301 | (PF01131) | ||||
| 340100.Bpet1302 | (PF00145) | ||||
| 340100.Bpet1305 | (PF02899) | ||||
| 340100.Bpet1306 | (PF00145) | ||||
| 340100.Bpet1238 | (PF02515) | ||||
| 340100.Bpet4346 | PF01527 | ||||
| 340100.Bpet4345 | PF00665 | ||||
| 340100.Bpet1120 | (PF02515) | ||||
| 340100.Bpet1126 | PF01527 | ||||
| 340100.Bpet1425 | (PF01144) | ||||
| 340100.Bpet3992 | PF01527 | ||||
| 340100.Bpet1449 | (PF00145) | ||||
| 340100.Bpet1448 | (PF01131) | ||||
| 340100.Bpet1447 | (PF00436) | ||||
| 340100.Bpet1939 | (PF02515) | ||||
| 340100.Bpet3228 | + | ||||
| 340100.Bpet3160 | + | ||||
| 340100.Bpet3167 | PF01527 | ||||
| 340100.Bpet3767 | PF01527 | ||||
| 340100.Bpet3760 | PF01527 | ||||
| 340100.Bpet1337 | PF01527 | ||||
| 340100.Bpet1336 | (PF10014) | ||||
| 340100.Bpet1205 | PF00665 | ||||
| 340100.Bpet1207 | PF00665 | ||||
| 340100.Bpet4429 | + | ||||
| 340100.Bpet4355 | (PF02515) | ||||
| 340100.Bpet1113 | PF00665 | ||||
| 340100.Bpet3985 | PF01527 | ||||
| 340100.Bpet3988 | PF01527 | ||||
| 340100.Bpet2348 | + | ||||
| 340100.Bpet1455 | (PF00145) | ||||
| 340100.Bpet3504 | (PF02515) | ||||
| 340100.Bpet0852 | (PF02515) | ||||
| 340100.Bpet0850 | (PF03972) | ||||
| 340100.Bpet3431 | (PF02515) | ||||
| 340100.Bpet3758 | PF00665 | ||||
| 340100.Bpet4635 | PF01527 | ||||
| 340100.Bpet4180 | (PF01144) | ||||
| 340100.Bpet4161 | (PF02515) | ||||
| 340100.Bpet1109 | PF01527 | ||||
| 340100.Bpet1106 | PF00665 | ||||
| 340100.Bpet4291 | PF01527 | ||||
| 340100.Bpet1464 | PF01527 | ||||
| 340100.Bpet1916 | PF01527 | ||||
| 340100.Bpet2108 | + | ||||
| 340100.Bpet1261 | (PF02615) | ||||
| 340100.Bpet3208 | (PF02515) | ||||
| 340100.Bpet0197 | PF01527 | ||||
| 340100.Bpet0194 | PF01527 | ||||
| 340100.Bpet0198 | PF00665 | ||||
| 340100.Bpet2439 | PF01527 | ||||
| 340100.Bpet2437 | (PF13683) | ||||
| 340100.Bpet4285 | (PF01348) | ||||
| 340100.Bpet0507 | PF01527 | ||||
| 340100.Bpet1475 | (PF01348) | ||||
| 340100.Bpet2118 | PF01527 | ||||
| 340100.Bpet2113 | PF01527 | ||||
| 340100.Bpet1494 | PF01527 | ||||
| 340100.Bpet1496 | + | ||||
| 340100.Bpet3733 | PF00665 | ||||
| 340100.Bpet0470 | (PF02515) | ||||
| 340100.Bpet4751 | + | ||||
| 340100.Bpet1019 | PF01527 | ||||
| 340100.Bpet0608 | (PF13683) | not used | |||
| 340100.Bpet0606 | PF01527 | ||||
| 340100.Bpet0604 | PF00665 | ||||
| 340100.Bpet1802 | + | ||||
| 340100.Bpet0864 | (PF04752) | ||||
| 340100.Bpet0862 | PF01527 | ||||
| 340100.Bpet0861 | (PF04752) | ||||
| 340100.Bpet3720 | PF01527 | ||||
| 340100.Bpet4816 | PF01527 | ||||
| 340100.Bpet1426 | (PF01144) | ||||
| 340100.Bpet1812 | (PF03972) | ||||
| 340100.Bpet0048 | (PF07287) | ||||
| 340100.Bpet4601 | PF00665 | ||||
| 340100.Bpet3651 | (PF02615) | ||||
| 340100.Bpet4777 | (PF02515) | ||||
| 340100.Bpet4152 | (PF07287) | ||||
| 340100.Bpet1393 | (PF01144) | ||||
| 340100.Bpet0262 | (PF02515) | ||||
| 340100.Bpet3897 | (PF02515) | ||||
| 340100.Bpet1650 | (PF03972) | ||||
| 340100.Bpet3895 | (PF02515) | ||||
| 340100.Bpet0819 | (PF02515) |
Detailed merged results for each protein sequence
- Detailed merged results as table (merge_results.html)
- Detailed merged results as tab delimited file (merge_results.csv)
Individual results for each protein sequence
- T4SEpre bpbAac predictions (T4SEpre_bpbAac_FinalResult.csv)
- T4SEpre psAac predictions (T4SEpre_psAac_FinalResult.csv)
- EffectiveELD predictions (PROTEINS.ELD.TXT)
- Predotar predictions using animal/human model (Predotar_output_modelANIMAL.TXT)
- Predotar predictions using plant model (Predotar_output_modelPLANT.TXT)
Genome based results
Summary
- Gram negative: YES (FDR = 0.5 %)
- Functional Type III secretion system: NO (FDR = 12.5 %)
- Functional Type IV secretion system: YES (FDR = 7.2 %)
Estimated copy number = 1.8 (18/10 KEGG proteins)
- Functional Type VI secretion system: YES (FDR = 7.7 %)
Estimated copy number = 1.75 (14/8 KEGG proteins)
Individual results for each secretion system
- List of 100 most important COGs/NOGs for prediction of functional Type III secretion system (T3_top100_COGS.xls)
- List of 100 most important COGs/NOGs for prediction of functional Type IV secretion system (T4_top100_COGS.xls)
- List of 100 most important COGs/NOGs for prediction of functional Type VI secretion system (T6_top100_COGS.xls)
- List of COGs assigned to Type III secretion system in KEGG (T3SS_KEGG_cmp.xls)
- List of COGs assigned to Type IV secretion system in KEGG (T4SS_KEGG_cmp.xls)
- List of COGs assigned to Type VI secretion system in KEGG (T6SS_KEGG_cmp.xls)
Parameters:
==========================================================
EFFECTIVE_T3_OLD=selective
EFFECTIVE_T3_NEW=selective
PREDOTAR_ANIMAL_OR_PLANT=a
PROTEINS=INPUT PROTEINS
MODUS=genome
RUN_PREDOTAR=T
RUN_EFFECTIVE_T3=T
RUN_T4SEpre=0.5
RUN_EFFECTIVE_CCBD=T
RUN_EFFECTIVE_ELD=4
CheckM_COMPLETENESS=
RUN_EffectiveS346=T
GENOTYPE=COG Profile
EMAIL=
==========================================================
Estimated copy number = 1.8 (18/10 KEGG proteins)
Estimated copy number = 1.75 (14/8 KEGG proteins)
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