Effective results for Methylobacterium extorquens AM1 (eggnog40)
Summary
Number of putative secreted proteins: 125
- Predicted by T4SEpre: 96
- Predicted by EffectiveELD: 17 eukaryotic-like domains, contained in 44 proteins (1 high, 43 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 |
---|---|---|---|---|---|
272630.MexAM1_META1p1929 | + | ER | |||
272630.MexAM1_META1p2203 | + | ER | |||
272630.MexAM1_META1p3912 | + | (ER) | |||
272630.MexAM1_META1p4456 | + | ER | |||
272630.MexAM1_META1p3228 | (PF01774) | (mitochondrial) | |||
272630.MexAM1_META1p2314 | + | ER | |||
272630.MexAM1_META1p5268 | (PF03209) | ER | |||
272630.MexAM1_META1p2412 | + | (mitochondrial); (plastid) | |||
272630.MexAM1_META1p1200 | (PF02683) | ER | |||
272630.MexAM1_META1p2639 | + | ER | |||
272630.MexAM1_META1p5039 | + | ER | |||
272630.MexAM1_META1p2246 | + | ER | |||
272630.MexAM1_META1p2646 | (PF02683) | (ER); (plastid) | |||
272630.MexAM1_META1p4772 | PF05769 | (mitochondrial) | |||
272630.MexAM1_META1p2329 | + | (ER) | |||
272630.MexAM1_META1p1224 | (PF03404) | ER | |||
272630.MexAM1_META1p1227 | (PF03404) | mitochondrial | |||
272630.MexAM1_META1p0037 | + | mitochondrial | |||
272630.MexAM1_META1p0661 | + | ER | |||
272630.MexAM1_META1p5185 | + | ER | |||
272630.MexAM1_META1p1498 | + | ER; (mitochondrial) | |||
272630.MexAM1_META1p0234 | + | ER; (ER) | |||
272630.MexAM1_META1p0078 | (PF02683) | ER | |||
272630.MexAM1_META1p5226 | + | (mitochondrial) | |||
272630.MexAM1_META1p0699 | + | mitochondrial | |||
272630.MexAM1_META1p0690 | + | ER | |||
272630.MexAM1_META1p1484 | + | (ER) | |||
272630.MexAM1_META1p1241 | (PF02683) | ER | |||
272630.MexAM1_META1p1033 | + | (mitochondrial) | |||
272630.MexAM1_META1p2598 | (PF02683) | ER | |||
272630.MexAM1_META1p4984 | + | ER | |||
272630.MexAM1_META1p2578 | + | ER | |||
272630.MexAM1_META1p1587 | (PF08892) | (mitochondrial); mitochondrial | |||
272630.MexAM1_META1p1292 | + | ER | |||
272630.MexAM1_META1p3607 | + | (ER) | |||
272630.MexAM1_META1p2580 | (PF02683) | ER | |||
272630.MexAM1_META1p1265 | + | ER | |||
272630.MexAM1_META1p3476 | + | (mitochondrial); (ER) | |||
272630.MexAM1_META1p3322 | + | mitochondrial | |||
272630.MexAM1_META1p3369 | (PF11911) | ER | |||
272630.MexAM1_META1p2382 | + | (mitochondrial) | |||
272630.MexAM1_META1p0640 | + | ER | |||
272630.MexAM1_META1p0359 | + | (ER) | |||
272630.MexAM1_META1p0395 | + | ER | |||
272630.MexAM1_META1p2626 | (PF02683) | (ER) | |||
272630.MexAM1_META1p0971 | (PF10908) | ER | |||
272630.MexAM1_META1p3390 | + | (ER); ER | |||
272630.MexAM1_META1p3142 | + | ER | |||
272630.MexAM1_META1p1171 | + | ER | |||
272630.MexAM1_META1p2040 | + | (ER) | |||
272630.MexAM1_META1p4174 | + | ER | |||
272630.MexAM1_META1p4444 | + | ER | |||
272630.MexAM1_META1p1564 | + | ER | |||
272630.MexAM1_META1p0228 | + | ER | |||
272630.MexAM1_META1p2304 | + | mitochondrial; (mitochondrial) | |||
272630.MexAM1_META1p5224 | + | (mitochondrial) | |||
272630.MexAM1_META1p2979 | + | (mitochondrial) | |||
272630.MexAM1_META1p2558 | (PF02683) | (ER) | |||
272630.MexAM1_META1p2948 | + | (mitochondrial) | |||
272630.MexAM1_META1p0403 | + | (mitochondrial) | |||
272630.MexAM1_META1p0297 | + | (ER) | |||
272630.MexAM1_META1p4913 | (PF01442) | ||||
272630.MexAM1_META1p4917 | + | ||||
272630.MexAM1_META1p2478 | + | ||||
272630.MexAM1_META1p3822 | + | ||||
272630.MexAM1_META1p1757 | + | ||||
272630.MexAM1_META1p5278 | (PF03209) | ||||
272630.MexAM1_META1p2889 | + | ||||
272630.MexAM1_META1p5181 | (PF05532) | ||||
272630.MexAM1_META1p1330 | + | ||||
272630.MexAM1_META1p0489 | + | ||||
272630.MexAM1_META1p4921 | + | ||||
272630.MexAM1_META1p2427 | (PF08892) | ||||
272630.MexAM1_META1p0300 | + | ||||
272630.MexAM1_META1p0270 | + | ||||
272630.MexAM1_META1p0277 | (PF05532) | ||||
272630.MexAM1_META1p0276 | (PF05532) | not used | |||
272630.MexAM1_META1p0279 | (PF05532) | ||||
272630.MexAM1_META1p1250 | (PF08797) | ||||
272630.MexAM1_META1p5227 | + | ||||
272630.MexAM1_META1p3222 | (PF01730) | ||||
272630.MexAM1_META1p2126 | (PF05532) | ||||
272630.MexAM1_META1p2218 | + | ||||
272630.MexAM1_META1p1067 | (PF01774) | ||||
272630.MexAM1_META1p1069 | (PF01730) | ||||
272630.MexAM1_META1p0991 | (PF07250) | ||||
272630.MexAM1_META1p2804 | + | ||||
272630.MexAM1_META1p3331 | + | ||||
272630.MexAM1_META1p4187 | + | ||||
272630.MexAM1_META1p2906 | (PF14701) | ||||
272630.MexAM1_META1p0380 | + | ||||
272630.MexAM1_META1p3988 | (PF13392) | ||||
272630.MexAM1_META1p0983 | (PF10908) | ||||
272630.MexAM1_META1p2311 | + | ||||
272630.MexAM1_META1p3182 | + | ||||
272630.MexAM1_META1p2567 | (PF03404) | ||||
272630.MexAM1_META1p2120 | + | ||||
272630.MexAM1_META1p4852 | + | ||||
272630.MexAM1_META1p2855 | + | ||||
272630.MexAM1_META1p5285 | + | ||||
272630.MexAM1_META1p5288 | + | ||||
272630.MexAM1_META1p3945 | (PF13392) | ||||
272630.MexAM1_META1p4085 | + | ||||
272630.MexAM1_META1p1986 | + | ||||
272630.MexAM1_META1p2169 | + | ||||
272630.MexAM1_META1p2381 | + | ||||
272630.MexAM1_META1p1448 | (PF11911) | ||||
272630.MexAM1_META1p3950 | (PF13392) | ||||
272630.MexAM1_META1p0574 | (PF12513) | ||||
272630.MexAM1_META1p1741 | + | ||||
272630.MexAM1_META1p2710 | + | ||||
272630.MexAM1_META1p0978 | (PF01774) | ||||
272630.MexAM1_META1p0974 | (PF01730) | ||||
272630.MexAM1_META1p3399 | + | ||||
272630.MexAM1_META1p0706 | + | ||||
272630.MexAM1_META1p0885 | + | ||||
272630.MexAM1_META1p0280 | (PF05532) | ||||
272630.MexAM1_META1p3558 | (PF03404) | ||||
272630.MexAM1_META1p0829 | (PF10013) | not used | |||
272630.MexAM1_META1p2460 | (PF05532) | ||||
272630.MexAM1_META1p1561 | (PF08797) | ||||
272630.MexAM1_META1p0624 | + | ||||
272630.MexAM1_META1p2857 | + | ||||
272630.MexAM1_META1p0610 | + | ||||
272630.MexAM1_META1p1923 | + |
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)