Effective results for Herbaspirillum seropedicae SmR1 (eggnog40)
Summary
Number of putative secreted proteins: 158
- Predicted by T4SEpre: 92
- Predicted by EffectiveELD: 10 eukaryotic-like domains, contained in 86 proteins (42 high, 44 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)
Protein based results
Putative secreted proteins (weak evidence indicated by parentheses)
| Protein | EffectiveT3 | EffectiveCCBD | T4SEpre | EffectiveELD | Predotar |
|---|---|---|---|---|---|
| 757424.Hsero_2726 | + | PF12729 (PF00015) | (mitochondrial); mitochondrial | ||
| 757424.Hsero_3032 | + | PF12729 (PF00015) | (ER); (mitochondrial) | ||
| 757424.Hsero_4656 | + | PF12729 (PF00015) | ER | ||
| 757424.Hsero_0538 | + | PF12729 (PF00015) | ER | ||
| 757424.Hsero_3966 | + | PF12729 (PF00015) | ER | ||
| 757424.Hsero_2619 | PF12729 (PF00015) | (ER) | |||
| 757424.Hsero_4615 | PF12729 (PF00015) | (ER); (mitochondrial) | |||
| 757424.Hsero_0455 | PF12729 (PF00015) | ER | |||
| 757424.Hsero_1659 | + | (PF13539) | ER | ||
| 757424.Hsero_1251 | PF12729 (PF00015) | ER | |||
| 757424.Hsero_3434 | PF12729 (PF00015) | ER | |||
| 757424.Hsero_2914 | PF12729 (PF00015) | ER; (ER) | |||
| 757424.Hsero_2915 | PF12729 (PF00015) | ER | |||
| 757424.Hsero_2723 | PF12729 (PF00015) | ER | |||
| 757424.Hsero_0720 | PF12729 (PF00015) | ER | |||
| 757424.Hsero_0394 | PF12729 (PF00015) | ER | |||
| 757424.Hsero_4025 | PF12729 (PF00015) | ER | |||
| 757424.Hsero_0030 | PF12729 (PF00015) | ER | |||
| 757424.Hsero_2671 | PF12729 (PF00015) | ER | |||
| 757424.Hsero_2662 | PF12729 (PF00015) | ER | |||
| 757424.Hsero_2299 | PF12729 (PF00015) | ER | |||
| 757424.Hsero_1361 | PF12729 (PF00015) | (ER) | |||
| 757424.Hsero_3124 | PF12729 (PF00015) | ER | |||
| 757424.Hsero_3022 | PF12729 (PF00015) | ER | |||
| 757424.Hsero_1095 | PF12729 (PF00015) | ER | |||
| 757424.Hsero_4780 | PF12729 (PF00015) | ER | |||
| 757424.Hsero_1336 | PF12729 (PF00015) | ER | |||
| 757424.Hsero_4643 | PF12729 (PF00015) | ER; (ER) | |||
| 757424.Hsero_1141 | PF12729 (PF00015) | (mitochondrial) | |||
| 757424.Hsero_1457 | PF12729 (PF00015) | ER | |||
| 757424.Hsero_3943 | PF12729 (PF00015) | ER; (ER) | |||
| 757424.Hsero_0623 | + | (PF00015) | ER | ||
| 757424.Hsero_1683 | PF12729 (PF00015) | ER | |||
| 757424.Hsero_1262 | PF12729 (PF00015) | ER; mitochondrial | |||
| 757424.Hsero_3755 | PF12729 (PF00015) | ER; mitochondrial | |||
| 757424.Hsero_4538 | PF12729 (PF00015) | ER; (ER) | |||
| 757424.Hsero_2577 | + | mitochondrial | |||
| 757424.Hsero_1878 | + | ER | |||
| 757424.Hsero_4543 | (PF00015) | ER | |||
| 757424.Hsero_4183 | + | ER | |||
| 757424.Hsero_2606 | (PF16387) | ER | |||
| 757424.Hsero_3730 | PF12729 (PF00015) | (mitochondrial) | |||
| 757424.Hsero_4609 | (PF00015) | ER | |||
| 757424.Hsero_0451 | + | ER | |||
| 757424.Hsero_1255 | + | (ER) | |||
| 757424.Hsero_1250 | (PF00015) | ER | |||
| 757424.Hsero_1252 | (PF00015) | ER | |||
| 757424.Hsero_4700 | (PF06884) | (ER) | |||
| 757424.Hsero_4019 | (PF00015) | ER | |||
| 757424.Hsero_2438 | (PF00015) | mitochondrial | |||
| 757424.Hsero_0139 | + | (mitochondrial) | |||
| 757424.Hsero_4174 | + | ER | |||
| 757424.Hsero_4371 | + | ER; (mitochondrial) | |||
| 757424.Hsero_0382 | + | (mitochondrial) | |||
| 757424.Hsero_3523 | (PF00015) | ER | |||
| 757424.Hsero_3700 | + | mitochondrial | |||
| 757424.Hsero_4388 | + | ER | |||
| 757424.Hsero_1730 | (PF07819) | (mitochondrial) | |||
| 757424.Hsero_1288 | PF12729 (PF00015) | (mitochondrial) | |||
| 757424.Hsero_1515 | (PF13436) | ER; (ER) | |||
| 757424.Hsero_0259 | (PF00015) | ER | |||
| 757424.Hsero_4730 | + | ER | |||
| 757424.Hsero_4026 | (PF13539) | ER | |||
| 757424.Hsero_0032 | + | (mitochondrial) | |||
| 757424.Hsero_1729 | + | ER | |||
| 757424.Hsero_4610 | + | ER | |||
| 757424.Hsero_4558 | + | ER | |||
| 757424.Hsero_3334 | + | mitochondrial | |||
| 757424.Hsero_1112 | + | ER | |||
| 757424.Hsero_1197 | + | ER | |||
| 757424.Hsero_2474 | PF12729 | ER | |||
| 757424.Hsero_2473 | (PF00015) | ER | |||
| 757424.Hsero_2270 | + | ER | |||
| 757424.Hsero_0165 | + | ER | |||
| 757424.Hsero_0761 | (PF13539) | ER | |||
| 757424.Hsero_1363 | (PF00015) | (ER) | |||
| 757424.Hsero_0835 | (PF00015) | (mitochondrial); plastid | |||
| 757424.Hsero_4046 | + | (mitochondrial) | |||
| 757424.Hsero_4672 | + | (ER) | |||
| 757424.Hsero_1794 | + | (mitochondrial) | |||
| 757424.Hsero_0900 | + | (mitochondrial) | |||
| 757424.Hsero_0915 | + | ER | |||
| 757424.Hsero_3488 | (PF00015) | ER | |||
| 757424.Hsero_1302 | (PF00015) | ER | |||
| 757424.Hsero_3148 | (PF00015) | ER | |||
| 757424.Hsero_0372 | + | (mitochondrial) | |||
| 757424.Hsero_3234 | (PF00015) | ER | |||
| 757424.Hsero_0976 | (PF00015) | ER | |||
| 757424.Hsero_3773 | (PF00015) | ER | |||
| 757424.Hsero_4644 | (PF00015) | ER | |||
| 757424.Hsero_2019 | (PF00015) | mitochondrial | |||
| 757424.Hsero_3545 | (PF00015) | mitochondrial | |||
| 757424.Hsero_2164 | (PF00015) | ER | |||
| 757424.Hsero_3160 | (PF00015) | ER | |||
| 757424.Hsero_4250 | + | ER | |||
| 757424.Hsero_0138 | + | (mitochondrial) | |||
| 757424.Hsero_2176 | + | (mitochondrial) | |||
| 757424.Hsero_1556 | PF12729 (PF00015) | ||||
| 757424.Hsero_1708 | (PF00015) | (ER) | |||
| 757424.Hsero_4039 | + | (ER) | |||
| 757424.Hsero_0733 | + | (ER) | |||
| 757424.Hsero_0787 | + | (plastid) | |||
| 757424.Hsero_4595 | PF12729 (PF00015) | ||||
| 757424.Hsero_1418 | + | (ER) | |||
| 757424.Hsero_2859 | + | (plastid) | |||
| 757424.Hsero_0183 | + | ||||
| 757424.Hsero_1129 | + | ||||
| 757424.Hsero_1698 | (PF00015) | ||||
| 757424.Hsero_1696 | + | ||||
| 757424.Hsero_2976 | + | ||||
| 757424.Hsero_3428 | + | ||||
| 757424.Hsero_2366 | + | ||||
| 757424.Hsero_3648 | + | ||||
| 757424.Hsero_4424 | PF16994 | ||||
| 757424.Hsero_4421 | PF01762 | ||||
| 757424.Hsero_4422 | PF16994 | ||||
| 757424.Hsero_4280 | + | ||||
| 757424.Hsero_1847 | + | ||||
| 757424.Hsero_2635 | + | ||||
| 757424.Hsero_3720 | (PF00015) | ||||
| 757424.Hsero_0286 | + | ||||
| 757424.Hsero_0448 | (PF00015) | ||||
| 757424.Hsero_2281 | + | ||||
| 757424.Hsero_4229 | + | ||||
| 757424.Hsero_2625 | + | ||||
| 757424.Hsero_3095 | + | ||||
| 757424.Hsero_0472 | + | ||||
| 757424.Hsero_1706 | (PF00015) | ||||
| 757424.Hsero_2770 | + | ||||
| 757424.Hsero_3063 | + | ||||
| 757424.Hsero_3840 | (PF00015) | ||||
| 757424.Hsero_0736 | + | ||||
| 757424.Hsero_3604 | + | ||||
| 757424.Hsero_4134 | + | ||||
| 757424.Hsero_3072 | (PF00015) | ||||
| 757424.Hsero_0929 | (PF13816) | ||||
| 757424.Hsero_4581 | + | ||||
| 757424.Hsero_0024 | (PF07819) | ||||
| 757424.Hsero_0021 | (PF07819) | ||||
| 757424.Hsero_1195 | + | ||||
| 757424.Hsero_0110 | + | ||||
| 757424.Hsero_2667 | + | ||||
| 757424.Hsero_0514 | (PF00015) | ||||
| 757424.Hsero_0836 | + | ||||
| 757424.Hsero_4322 | (PF07819) | ||||
| 757424.Hsero_4105 | + | ||||
| 757424.Hsero_2227 | + | ||||
| 757424.Hsero_0229 | (PF13539) | ||||
| 757424.Hsero_0173 | + | ||||
| 757424.Hsero_2194 | + | ||||
| 757424.Hsero_0913 | + | ||||
| 757424.Hsero_4441 | + | ||||
| 757424.Hsero_3923 | + | ||||
| 757424.Hsero_4173 | + | ||||
| 757424.Hsero_2532 | + | ||||
| 757424.Hsero_1897 | + | ||||
| 757424.Hsero_1330 | (PF00015) | ||||
| 757424.Hsero_2024 | + |
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 = 0.0 (0/10 KEGG proteins)
- Functional Type VI secretion system: NO (FDR = 7.7 %)
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 = 0.0 (0/10 KEGG proteins)
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