Effective results for Nitrobacter hamburgensis X14 (eggnog40)
Summary
Number of putative secreted proteins: 211
- Predicted by T4SEpre: 106
- Predicted by EffectiveELD: 21 eukaryotic-like domains, contained in 129 proteins (71 high, 58 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 |
|---|---|---|---|---|---|
| 323097.Nham_1628 | PF13565 (PF13358) | mitochondrial | |||
| 323097.Nham_1627 | PF13565 (PF13358) | mitochondrial | |||
| 323097.Nham_2447 | PF13565 (PF13358) | mitochondrial | |||
| 323097.Nham_3168 | PF13565 (PF13358) | mitochondrial | |||
| 323097.Nham_2888 | + | (PF05239) | ER | ||
| 323097.Nham_3014 | + | PF13565 | mitochondrial | ||
| 323097.Nham_3871 | + | (PF02735) | (mitochondrial); mitochondrial | ||
| 323097.Nham_0871 | PF13565 (PF13358) | mitochondrial | |||
| 323097.Nham_2516 | PF13565 (PF13358) | mitochondrial | |||
| 323097.Nham_2834 | PF13565 (PF13358) | mitochondrial | |||
| 323097.Nham_3895 | PF13565 (PF13358) | mitochondrial | |||
| 323097.Nham_0486 | + | mitochondrial; (mitochondrial) | |||
| 323097.Nham_3676 | + | ER | |||
| 323097.Nham_1539 | + | (mitochondrial) | |||
| 323097.Nham_3850 | (PF00386) | ER | |||
| 323097.Nham_0251 | (PF14295) | (ER) | |||
| 323097.Nham_0809 | PF13565 (PF13358) | (plastid) | |||
| 323097.Nham_3917 | (PF02735) | (mitochondrial); mitochondrial | |||
| 323097.Nham_1462 | + | (mitochondrial) | |||
| 323097.Nham_2437 | + | (mitochondrial) | |||
| 323097.Nham_2941 | PF12142 | (mitochondrial) | |||
| 323097.Nham_0651 | (PF04442) | ER | |||
| 323097.Nham_3229 | + | mitochondrial | |||
| 323097.Nham_2760 | + | (ER); (mitochondrial) | |||
| 323097.Nham_3906 | (PF02735) | mitochondrial | |||
| 323097.Nham_3580 | (PF05239) | (mitochondrial) | |||
| 323097.Nham_0836 | + | (ER) | |||
| 323097.Nham_3935 | + | (mitochondrial); mitochondrial | |||
| 323097.Nham_1264 | PF13565 | (mitochondrial) | |||
| 323097.Nham_2561 | + | mitochondrial | |||
| 323097.Nham_0772 | + | ER; (mitochondrial) | |||
| 323097.Nham_0355 | + | (mitochondrial) | |||
| 323097.Nham_0450 | (PF02735) | (mitochondrial); mitochondrial | |||
| 323097.Nham_3791 | + | (mitochondrial) | |||
| 323097.Nham_2686 | (PF00839) | ER | |||
| 323097.Nham_3065 | (PF01695) | (mitochondrial) | |||
| 323097.Nham_3201 | + | (mitochondrial) | |||
| 323097.Nham_1685 | + | ER | |||
| 323097.Nham_1133 | + | ER | |||
| 323097.Nham_0080 | + | (mitochondrial) | |||
| 323097.Nham_3642 | + | mitochondrial | |||
| 323097.Nham_0214 | + | ER | |||
| 323097.Nham_2237 | + | ER | |||
| 323097.Nham_2837 | PF13565 | (mitochondrial); (plastid) | |||
| 323097.Nham_3075 | (PF01609) | mitochondrial | |||
| 323097.Nham_0418 | + | mitochondrial; (plastid) | |||
| 323097.Nham_0419 | (PF05239) | ER | |||
| 323097.Nham_1591 | (PF00565) | ER | |||
| 323097.Nham_2677 | + | mitochondrial; (mitochondrial) | |||
| 323097.Nham_3234 | + | (mitochondrial) | |||
| 323097.Nham_3982 | (PF01609) | ER | |||
| 323097.Nham_3622 | + | ER | |||
| 323097.Nham_1969 | (PF00565) | ER | |||
| 323097.Nham_1811 | + | ER | |||
| 323097.Nham_3735 | + | mitochondrial | |||
| 323097.Nham_3956 | (PF00565) | ER | |||
| 323097.Nham_0992 | + | ER | |||
| 323097.Nham_0604 | (PF00839) | ER | |||
| 323097.Nham_2864 | + | ER | |||
| 323097.Nham_3391 | PF05598 (PF01609) | ||||
| 323097.Nham_3140 | PF05598 (PF01609) | ||||
| 323097.Nham_2160 | PF05598 (PF01609) | ||||
| 323097.Nham_3290 | PF05598 (PF01609) | ||||
| 323097.Nham_1473 | PF05598 (PF01609) | ||||
| 323097.Nham_3113 | PF05598 (PF01609) | ||||
| 323097.Nham_3552 | PF05598 (PF01609) | ||||
| 323097.Nham_1266 | PF05598 (PF01609) | ||||
| 323097.Nham_2748 | PF05598 (PF01609) | ||||
| 323097.Nham_4022 | (PF00102) | (plastid) | |||
| 323097.Nham_1095 | PF05598 (PF01609) | ||||
| 323097.Nham_3654 | PF05598 (PF01609) | ||||
| 323097.Nham_3308 | (PF05239) | (mitochondrial) | |||
| 323097.Nham_1653 | PF05598 (PF01609) | ||||
| 323097.Nham_3414 | PF05598 (PF01609) | ||||
| 323097.Nham_0898 | (PF11523) | (mitochondrial) | |||
| 323097.Nham_1135 | PF05598 (PF01609) | ||||
| 323097.Nham_3853 | (PF05239) | (mitochondrial) | |||
| 323097.Nham_0259 | + | (PF04442) | |||
| 323097.Nham_1692 | (PF01609) | plastid | |||
| 323097.Nham_0965 | + | (ER) | |||
| 323097.Nham_3440 | PF05598 (PF01609) | ||||
| 323097.Nham_3459 | + | (PF04442) | |||
| 323097.Nham_0512 | PF05598 (PF01609) | ||||
| 323097.Nham_1821 | PF05598 (PF01609) | ||||
| 323097.Nham_3090 | (PF00565) | (mitochondrial) | |||
| 323097.Nham_0701 | PF05598 (PF01609) | ||||
| 323097.Nham_1498 | PF05598 (PF01609) | ||||
| 323097.Nham_2596 | PF05598 (PF01609) | ||||
| 323097.Nham_3715 | (PF01695) | ||||
| 323097.Nham_0571 | + | ||||
| 323097.Nham_1318 | (PF01442) | ||||
| 323097.Nham_1156 | (PF13358) | ||||
| 323097.Nham_0322 | (PF04098) | ||||
| 323097.Nham_0808 | PF02371 | ||||
| 323097.Nham_3948 | + | ||||
| 323097.Nham_4013 | (PF13358) | ||||
| 323097.Nham_0035 | + | ||||
| 323097.Nham_1639 | + | ||||
| 323097.Nham_0725 | + | ||||
| 323097.Nham_1037 | + | ||||
| 323097.Nham_2934 | PF02371 | ||||
| 323097.Nham_2150 | + | ||||
| 323097.Nham_1045 | + | ||||
| 323097.Nham_3289 | + | ||||
| 323097.Nham_0155 | + | ||||
| 323097.Nham_3826 | PF13565 | ||||
| 323097.Nham_1463 | + | ||||
| 323097.Nham_1999 | PF02371 | ||||
| 323097.Nham_2945 | + | ||||
| 323097.Nham_2361 | (PF05239) | ||||
| 323097.Nham_3769 | PF02371 | ||||
| 323097.Nham_0834 | PF02371 | ||||
| 323097.Nham_1188 | (PF13358) | ||||
| 323097.Nham_0900 | (PF01695) | ||||
| 323097.Nham_1056 | (PF01697) | ||||
| 323097.Nham_1152 | (PF05239) | ||||
| 323097.Nham_2955 | PF02371 | ||||
| 323097.Nham_1876 | + | ||||
| 323097.Nham_2773 | PF02371 | ||||
| 323097.Nham_2171 | (PF05239) | ||||
| 323097.Nham_3339 | + | ||||
| 323097.Nham_3931 | (PF05239) | ||||
| 323097.Nham_3939 | PF02371 | ||||
| 323097.Nham_0132 | PF02371 | ||||
| 323097.Nham_0910 | + | ||||
| 323097.Nham_3924 | (PF01695) | ||||
| 323097.Nham_0109 | PF02371 | ||||
| 323097.Nham_3814 | (PF05239) | ||||
| 323097.Nham_1305 | + | ||||
| 323097.Nham_2406 | + | ||||
| 323097.Nham_2998 | (PF01609) | ||||
| 323097.Nham_3348 | + | ||||
| 323097.Nham_2759 | PF05598 | ||||
| 323097.Nham_2758 | PF05598 | ||||
| 323097.Nham_3007 | PF02371 | ||||
| 323097.Nham_3794 | (PF05239) | ||||
| 323097.Nham_0208 | + | ||||
| 323097.Nham_3996 | PF02371 | ||||
| 323097.Nham_1428 | (PF06662) | ||||
| 323097.Nham_0247 | PF05598 | ||||
| 323097.Nham_0246 | (PF01609) | ||||
| 323097.Nham_2506 | (PF05239) | ||||
| 323097.Nham_2500 | (PF01609) | ||||
| 323097.Nham_1939 | PF02371 | ||||
| 323097.Nham_3788 | (PF01609) | ||||
| 323097.Nham_1783 | + | ||||
| 323097.Nham_0788 | (PF01695) | ||||
| 323097.Nham_3447 | + | ||||
| 323097.Nham_3468 | + | ||||
| 323097.Nham_3465 | + | ||||
| 323097.Nham_3060 | PF02371 | ||||
| 323097.Nham_3061 | (PF13358) | ||||
| 323097.Nham_3069 | + | ||||
| 323097.Nham_3682 | PF02371 | ||||
| 323097.Nham_0319 | (PF01695) | ||||
| 323097.Nham_1138 | + | ||||
| 323097.Nham_0081 | + | ||||
| 323097.Nham_3641 | + | ||||
| 323097.Nham_2306 | PF02371 | ||||
| 323097.Nham_2789 | PF13565 | ||||
| 323097.Nham_2786 | (PF01695) | ||||
| 323097.Nham_2012 | + | ||||
| 323097.Nham_3073 | + | ||||
| 323097.Nham_3079 | PF02371 | ||||
| 323097.Nham_0329 | + | ||||
| 323097.Nham_0748 | + | ||||
| 323097.Nham_1690 | PF05598 | ||||
| 323097.Nham_1340 | + | ||||
| 323097.Nham_2003 | (PF13358) | ||||
| 323097.Nham_3049 | + | ||||
| 323097.Nham_0302 | + | ||||
| 323097.Nham_3994 | + | ||||
| 323097.Nham_3995 | PF02371 | ||||
| 323097.Nham_3993 | + | ||||
| 323097.Nham_0531 | + | ||||
| 323097.Nham_1203 | (PF01695) | ||||
| 323097.Nham_1590 | + | ||||
| 323097.Nham_2499 | PF05598 | ||||
| 323097.Nham_1373 | + | ||||
| 323097.Nham_1376 | PF05598 | ||||
| 323097.Nham_1378 | PF02371 | ||||
| 323097.Nham_3058 | PF02371 | ||||
| 323097.Nham_3235 | + | ||||
| 323097.Nham_0509 | (PF00565) | ||||
| 323097.Nham_0506 | + | ||||
| 323097.Nham_1018 | + | ||||
| 323097.Nham_1568 | + | ||||
| 323097.Nham_1364 | + | ||||
| 323097.Nham_2245 | + | ||||
| 323097.Nham_1815 | + | ||||
| 323097.Nham_3913 | (PF01695) | ||||
| 323097.Nham_3085 | PF02371 | ||||
| 323097.Nham_3083 | PF02371 | ||||
| 323097.Nham_3889 | PF05598 | ||||
| 323097.Nham_3955 | PF02371 | ||||
| 323097.Nham_3980 | (PF05239) | ||||
| 323097.Nham_2470 | + | ||||
| 323097.Nham_1954 | PF02371 | ||||
| 323097.Nham_1959 | PF02371 | ||||
| 323097.Nham_2272 | PF02371 | ||||
| 323097.Nham_2723 | + | ||||
| 323097.Nham_2910 | + | ||||
| 323097.Nham_0613 | + | ||||
| 323097.Nham_3437 | (PF13358) | ||||
| 323097.Nham_3943 | PF02371 | ||||
| 323097.Nham_3898 | + | ||||
| 323097.Nham_0013 | PF05598 | ||||
| 323097.Nham_0014 | (PF01609) | ||||
| 323097.Nham_0946 | + | ||||
| 323097.Nham_0943 | + | ||||
| 323097.Nham_2267 | PF04184 |
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 = 0.1 (1/10 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 = 0.1 (1/10 KEGG proteins)
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