Effective results for Sphingobium sp. SYK-6 (eggnog40)
Summary
Number of putative secreted proteins: 168
- Predicted by T4SEpre: 42
- Predicted by EffectiveELD: 19 eukaryotic-like domains, contained in 130 proteins (53 high, 77 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 |
---|---|---|---|---|---|
627192.SLG_12660 | (PF12680) | ER | |||
627192.SLG_19100 | (PF12680) | ER | |||
627192.SLG_28140 | PF13577 | (ER) | |||
627192.SLG_18190 | (PF05960) | ER | |||
627192.SLG_04380 | + | ER | |||
627192.SLG_12120 | PF13577 | ER | |||
627192.SLG_13550 | (PF05960) | ER | |||
627192.SLG_15250 | PF13577 | ER | |||
627192.SLG_02610 | + | (mitochondrial) | |||
627192.SLG_28840 | (PF04909) | ER; (ER) | |||
627192.SLG_28660 | PF11578 | ER | |||
627192.SLG_15280 | PF13577 | mitochondrial | |||
627192.SLG_11840 | (PF09825) | (mitochondrial) | |||
627192.SLG_11660 | + | mitochondrial; (mitochondrial) | |||
627192.SLG_28640 | + | ER | |||
627192.SLG_26310 | PF13577 | ER | |||
627192.SLG_31230 | PF13577 | ER | |||
627192.SLG_35220 | (PF04862) | ER | |||
627192.SLG_32340 | (PF05960) | ER | |||
627192.SLG_04310 | + | (mitochondrial) | |||
627192.SLG_20870 | + | ER | |||
627192.SLG_18820 | + | mitochondrial | |||
627192.SLG_12230 | PF13577 | ER | |||
627192.SLG_32180 | PF13577 | ER | |||
627192.SLG_16840 | PF05735 | (ER) | |||
627192.SLG_36710 | PF13577 | ER; (mitochondrial) | |||
627192.SLG_28120 | PF13577 | ER | |||
627192.SLG_18670 | (PF12680) | ER | |||
627192.SLG_08220 | (PF05960) | ER | |||
627192.SLG_36720 | PF13577 | ER | |||
627192.SLG_01820 | + | mitochondrial | |||
627192.SLG_12250 | PF13577 | ER | |||
627192.SLG_27320 | + | mitochondrial; (mitochondrial) | |||
627192.SLG_32720 | + | ER | |||
627192.SLG_36730 | PF13577 | ER | |||
627192.SLG_37350 | + | (mitochondrial) | |||
627192.SLG_37600 | + | ER | |||
627192.SLG_12240 | PF13577 | ER | |||
627192.SLG_33510 | (PF05960) | ER | |||
627192.SLG_30740 | + | ER | |||
627192.SLG_18790 | (PF12680) | ER | |||
627192.SLG_31290 | PF13577 | ER | |||
627192.SLG_23070 | (PF06455) | ER | |||
627192.SLG_25890 | (PF05960) | ER | |||
627192.SLG_34470 | (PF05960) | (ER) | |||
627192.SLG_12670 | (PF12680) | ER | |||
627192.SLG_15000 | (PF04800) | (mitochondrial) | |||
627192.SLG_28110 | PF13577 | (mitochondrial) | |||
627192.SLG_20100 | + | PF13577 | |||
627192.SLG_07720 | (PF02900) | (plastid) | |||
627192.SLG_18560 | PF13577 | (mitochondrial) | |||
627192.SLG_21800 | + | (mitochondrial) | |||
627192.SLG_27990 | PF13577 | (ER) | |||
627192.SLG_12100 | PF13577 | (plastid) | |||
627192.SLG_09410 | PF13577 | ||||
627192.SLG_36350 | + | ||||
627192.SLG_27970 | PF03055 | ||||
627192.SLG_06620 | PF13577 | ||||
627192.SLG_23260 | (PF12680) | ||||
627192.SLG_36670 | + | ||||
627192.SLG_18420 | PF13577 | ||||
627192.SLG_36960 | + | ||||
627192.SLG_30010 | (PF12680) | ||||
627192.SLG_13520 | + | ||||
627192.SLG_09890 | (PF12680) | ||||
627192.SLG_07030 | (PF13281) | ||||
627192.SLG_31300 | (PF04909) | ||||
627192.SLG_19550 | + | ||||
627192.SLG_08670 | PF16865 | ||||
627192.SLG_21700 | + | ||||
627192.SLG_35940 | (PF04909) | ||||
627192.SLG_19020 | (PF04909) | ||||
627192.SLG_07900 | (PF12831) | ||||
627192.SLG_03370 | (PF02900) | ||||
627192.SLG_06470 | (PF04909) | ||||
627192.SLG_23760 | (PF13759) | ||||
627192.SLG_09450 | (PF12680) | ||||
627192.SLG_23160 | (PF12680) | ||||
627192.SLG_19030 | (PF02900) | ||||
627192.SLG_27930 | PF13577 | ||||
627192.SLG_38060 | PF13577 | ||||
627192.SLG_22360 | + | ||||
627192.SLG_12570 | (PF04909) | ||||
627192.SLG_34850 | (PF04909) | ||||
627192.SLG_04620 | + | ||||
627192.SLG_10950 | (PF05189) | ||||
627192.SLG_21030 | (PF05960) | ||||
627192.SLG_07040 | + | ||||
627192.SLG_34960 | PF13577 | ||||
627192.SLG_27840 | (PF12680) | ||||
627192.SLG_09440 | PF03055 | ||||
627192.SLG_09530 | (PF12680) | ||||
627192.SLG_18930 | (PF04909) | ||||
627192.SLG_12500 | (PF02900) | ||||
627192.SLG_27250 | PF11578 | ||||
627192.SLG_07850 | (PF04909) | ||||
627192.SLG_31190 | + | ||||
627192.SLG_38040 | PF13577 | ||||
627192.SLG_22340 | + | ||||
627192.SLG_04480 | (PF12680) | ||||
627192.SLG_17610 | (PF12680) | ||||
627192.SLG_27240 | PF11578 | ||||
627192.SLG_11860 | (PF13759) | ||||
627192.SLG_26440 | + | ||||
627192.SLG_23350 | + | ||||
627192.SLG_15610 | (PF12831) | ||||
627192.SLG_27900 | (PF12680) | ||||
627192.SLG_27870 | (PF12680) | ||||
627192.SLG_12520 | (PF04909) | ||||
627192.SLG_13340 | + | ||||
627192.SLG_21820 | (PF13392) | ||||
627192.SLG_07890 | (PF12831) | ||||
627192.SLG_35080 | (PF04909) | ||||
627192.SLG_09360 | PF11578 | ||||
627192.SLG_09490 | (PF12680) | ||||
627192.SLG_12680 | (PF04909) | ||||
627192.SLG_22030 | + | ||||
627192.SLG_37540 | PF03055 | ||||
627192.SLG_26330 | (PF10703) | ||||
627192.SLG_10680 | + | ||||
627192.SLG_20090 | (PF12680) | ||||
627192.SLG_07880 | (PF12831) | ||||
627192.SLG_15360 | (PF04909) | ||||
627192.SLG_09370 | PF11578 | ||||
627192.SLG_27850 | PF11578 | ||||
627192.SLG_12780 | PF13577 | ||||
627192.SLG_37520 | (PF02900) | ||||
627192.SLG_12810 | (PF04909) | ||||
627192.SLG_17570 | PF13577 | ||||
627192.SLG_11300 | PF03055 | ||||
627192.SLG_06630 | (PF04909) | ||||
627192.SLG_31560 | + | ||||
627192.SLG_35000 | (PF04909) | ||||
627192.SLG_33520 | PF13577 | ||||
627192.SLG_36640 | PF03055 | ||||
627192.SLG_28100 | (PF04909) | ||||
627192.SLG_07750 | (PF04909) | ||||
627192.SLG_18650 | PF13577 | ||||
627192.SLG_12650 | PF13577 | ||||
627192.SLG_32480 | + | ||||
627192.SLG_27830 | (PF12680) | ||||
627192.SLG_19130 | (PF04909) | ||||
627192.SLG_01800 | (PF02900) | ||||
627192.SLG_26940 | + | ||||
627192.SLG_21640 | (PF13392) | ||||
627192.SLG_07290 | PF11578 | ||||
627192.SLG_03330 | (PF02900) | ||||
627192.SLG_27300 | PF03055 | ||||
627192.SLG_02060 | + | ||||
627192.SLG_26760 | (PF04800) | ||||
627192.SLG_15440 | + | ||||
627192.SLG_26370 | (PF10703) | ||||
627192.SLG_27480 | (PF12831) | ||||
627192.SLG_12460 | PF13577 | ||||
627192.SLG_27000 | + | ||||
627192.SLG_12860 | PF03055 | ||||
627192.SLG_18740 | PF13577 | ||||
627192.SLG_00500 | + | ||||
627192.SLG_31240 | PF13577 | ||||
627192.SLG_28570 | (PF04909) | ||||
627192.SLG_22040 | (PF13392) | ||||
627192.SLG_12580 | PF03055 | ||||
627192.SLG_12850 | PF11578 | ||||
627192.SLG_04940 | (PF12680) | ||||
627192.SLG_10160 | + | ||||
627192.SLG_05440 | (PF12680) | ||||
627192.SLG_07550 | (PF12831) | ||||
627192.SLG_09380 | (PF12680) |
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 = 1.2 (12/10 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 = 1.2 (12/10 KEGG proteins)