Effective results for Geobacter bemidjiensis Bem (eggnog40)
Summary
Number of putative secreted proteins: 248
- Predicted by T4SEpre: 0
- Predicted by EffectiveELD: 37 eukaryotic-like domains, contained in 248 proteins (1 high, 247 medium Z-score)
Predicted protein secretion systems (parentheses indicate weak positive predictions lacking more than 50% of core proteins of a secretion system): (Type VI)
Protein based results
Putative secreted proteins (weak evidence indicated by parentheses)
| Protein | EffectiveT3 | EffectiveCCBD | T4SEpre | EffectiveELD | Predotar |
|---|---|---|---|---|---|
| 404380.Gbem_1163 | (PF02310) (PF04055) | ER | |||
| 404380.Gbem_1463 | (PF02754) (PF13237) | (ER) | |||
| 404380.Gbem_2831 | (PF02754) (PF13237) | (ER) | |||
| 404380.Gbem_3387 | (PF02310) (PF04055) | (ER); (mitochondrial) | |||
| 404380.Gbem_3229 | (PF02754) (PF13237) | ER | |||
| 404380.Gbem_3304 | (PF02310) (PF04055) | (ER) | |||
| 404380.Gbem_2087 | (PF02754) (PF13237) | ER | |||
| 404380.Gbem_1358 | (PF00766) (PF13187) (PF01012) | ||||
| 404380.Gbem_1359 | (PF02754) | ER | |||
| 404380.Gbem_1227 | (PF00989) | ER | |||
| 404380.Gbem_4064 | (PF02224) | (mitochondrial) | |||
| 404380.Gbem_0907 | (PF04187) | ER | |||
| 404380.Gbem_1693 | (PF12849) | ER | |||
| 404380.Gbem_1502 | (PF02754) | ER | |||
| 404380.Gbem_1501 | (PF00766) (PF12838) (PF01012) | ||||
| 404380.Gbem_0259 | (PF00549) | (mitochondrial) | |||
| 404380.Gbem_1899 | (PF04055) | (mitochondrial) | |||
| 404380.Gbem_2870 | (PF05140) | ER | |||
| 404380.Gbem_0009 | (PF00989) | ER | |||
| 404380.Gbem_1750 | PF14874 | ER | |||
| 404380.Gbem_0600 | (PF00989) | ER | |||
| 404380.Gbem_1468 | (PF02754) | ER | |||
| 404380.Gbem_2069 | (PF00989) | ER | |||
| 404380.Gbem_3740 | (PF13176) | (ER); (mitochondrial) | |||
| 404380.Gbem_1710 | (PF12849) | ER | |||
| 404380.Gbem_1864 | (PF00989) | ER | |||
| 404380.Gbem_2226 | (PF00989) | (ER) | |||
| 404380.Gbem_2645 | (PF13176) | ER | |||
| 404380.Gbem_2137 | (PF00989) | ER; (ER) | |||
| 404380.Gbem_1716 | (PF12849) | ER | |||
| 404380.Gbem_3613 | (PF12849) | ER | |||
| 404380.Gbem_3612 | (PF12849) | ER | |||
| 404380.Gbem_3187 | (PF01058) | (mitochondrial) | |||
| 404380.Gbem_3508 | (PF04055) | (ER) | |||
| 404380.Gbem_0081 | (PF00989) | ER | |||
| 404380.Gbem_0647 | (PF12849) | ER | |||
| 404380.Gbem_1847 | (PF12849) | ER | |||
| 404380.Gbem_0648 | (PF12849) | ER | |||
| 404380.Gbem_1112 | (PF13176) | (ER) | |||
| 404380.Gbem_1852 | (PF12849) | ER | |||
| 404380.Gbem_3363 | (PF04055) | (mitochondrial) | |||
| 404380.Gbem_3966 | (PF05140) | ER | |||
| 404380.Gbem_0446 | (PF13176) | ER | |||
| 404380.Gbem_0534 | (PF04187) | ER | |||
| 404380.Gbem_3959 | (PF00989) | ER | |||
| 404380.Gbem_2951 | (PF00989) | ER | |||
| 404380.Gbem_0830 | (PF12838) | (mitochondrial) | |||
| 404380.Gbem_1491 | (PF12849) | ER | |||
| 404380.Gbem_0897 | (PF02310) (PF04055) | (ER) | |||
| 404380.Gbem_3051 | (PF00989) | (ER); ER | |||
| 404380.Gbem_0040 | (PF01814) | ER | |||
| 404380.Gbem_0820 | (PF13436) | ER | |||
| 404380.Gbem_1800 | (PF04862) | ER | |||
| 404380.Gbem_1806 | (PF13492) | ER | |||
| 404380.Gbem_2086 | (PF00766) (PF13187) (PF01012) | ||||
| 404380.Gbem_2155 | (PF00989) | ER | |||
| 404380.Gbem_3331 | (PF12849) | ER | |||
| 404380.Gbem_3202 | (PF16199) (PF04055) | (ER) | |||
| 404380.Gbem_0801 | (PF00989) | ER | |||
| 404380.Gbem_1354 | (PF04055) | (mitochondrial) | |||
| 404380.Gbem_2843 | (PF02550) (PF13336) | ||||
| 404380.Gbem_3467 | (PF02310) (PF04055) | ||||
| 404380.Gbem_3488 | (PF02310) (PF04055) | ||||
| 404380.Gbem_0905 | (PF00989) | (ER) | |||
| 404380.Gbem_1699 | (PF02310) (PF04055) | ||||
| 404380.Gbem_1165 | (PF02310) (PF04055) | ||||
| 404380.Gbem_1430 | (PF02550) (PF13336) | ||||
| 404380.Gbem_1439 | (PF02550) (PF13336) | ||||
| 404380.Gbem_3802 | (PF13237) | plastid | |||
| 404380.Gbem_1418 | (PF02550) (PF13336) | ||||
| 404380.Gbem_1467 | (PF00766) (PF01012) | ||||
| 404380.Gbem_1470 | (PF00766) (PF01012) | ||||
| 404380.Gbem_2829 | (PF00766) (PF01012) | ||||
| 404380.Gbem_3386 | (PF04055) | (mitochondrial) | |||
| 404380.Gbem_0093 | (PF02310) (PF04055) | ||||
| 404380.Gbem_0651 | (PF16199) (PF04055) | ||||
| 404380.Gbem_0878 | (PF02310) (PF04055) | ||||
| 404380.Gbem_1450 | (PF13187) | (mitochondrial) | |||
| 404380.Gbem_3769 | (PF16199) (PF04055) | ||||
| 404380.Gbem_0468 | (PF02550) (PF13336) | ||||
| 404380.Gbem_1029 | (PF02310) (PF04055) | ||||
| 404380.Gbem_1024 | (PF02310) (PF04055) | ||||
| 404380.Gbem_1334 | (PF00766) (PF01012) | ||||
| 404380.Gbem_3573 | (PF02550) (PF13336) | ||||
| 404380.Gbem_0067 | (PF01058) (PF13187) | ||||
| 404380.Gbem_3897 | (PF02550) (PF13336) | ||||
| 404380.Gbem_2318 | (PF03144) | (mitochondrial) | |||
| 404380.Gbem_3595 | (PF02310) (PF04055) | ||||
| 404380.Gbem_0795 | (PF02550) (PF13336) | ||||
| 404380.Gbem_1357 | (PF01012) | ||||
| 404380.Gbem_1226 | (PF12838) | ||||
| 404380.Gbem_1220 | (PF13565) | ||||
| 404380.Gbem_2845 | (PF00989) | ||||
| 404380.Gbem_3487 | (PF04055) | ||||
| 404380.Gbem_4067 | (PF12838) | ||||
| 404380.Gbem_0015 | (PF04055) | ||||
| 404380.Gbem_1760 | (PF04187) | ||||
| 404380.Gbem_0900 | (PF00989) | ||||
| 404380.Gbem_0747 | (PF01739) | ||||
| 404380.Gbem_0749 | (PF13492) | ||||
| 404380.Gbem_1509 | (PF02915) | ||||
| 404380.Gbem_1500 | (PF01012) | ||||
| 404380.Gbem_1168 | (PF03063) | ||||
| 404380.Gbem_1160 | (PF05140) | ||||
| 404380.Gbem_1987 | (PF13492) | ||||
| 404380.Gbem_1184 | (PF13187) | ||||
| 404380.Gbem_1188 | (PF02915) | ||||
| 404380.Gbem_1347 | (PF13565) | ||||
| 404380.Gbem_1436 | (PF04055) | ||||
| 404380.Gbem_1239 | (PF03063) | ||||
| 404380.Gbem_3962 | (PF00025) | ||||
| 404380.Gbem_2615 | (PF04055) | ||||
| 404380.Gbem_2050 | (PF04055) | ||||
| 404380.Gbem_2053 | (PF04055) | ||||
| 404380.Gbem_2272 | (PF04055) | ||||
| 404380.Gbem_2278 | (PF13187) | not used | |||
| 404380.Gbem_3870 | (PF01814) | ||||
| 404380.Gbem_3018 | (PF01814) | ||||
| 404380.Gbem_3878 | (PF00989) | ||||
| 404380.Gbem_0915 | (PF04055) | ||||
| 404380.Gbem_4034 | (PF12838) | ||||
| 404380.Gbem_4047 | (PF04055) | ||||
| 404380.Gbem_2515 | (PF13176) | ||||
| 404380.Gbem_2830 | (PF01012) | ||||
| 404380.Gbem_2262 | (PF01814) | ||||
| 404380.Gbem_2605 | (PF13492) | ||||
| 404380.Gbem_0618 | (PF04055) | ||||
| 404380.Gbem_0295 | (PF13492) | ||||
| 404380.Gbem_0433 | (PF13565) | ||||
| 404380.Gbem_1410 | (PF04055) | ||||
| 404380.Gbem_1252 | (PF01814) | ||||
| 404380.Gbem_1251 | (PF01814) | ||||
| 404380.Gbem_2079 | (PF12838) | ||||
| 404380.Gbem_2701 | (PF01814) | ||||
| 404380.Gbem_3257 | (PF02224) | ||||
| 404380.Gbem_2819 | (PF05189) | ||||
| 404380.Gbem_2497 | (PF01739) | ||||
| 404380.Gbem_2927 | (PF02754) | ||||
| 404380.Gbem_3724 | (PF04055) | ||||
| 404380.Gbem_0931 | (PF03144) | ||||
| 404380.Gbem_0930 | (PF03144) | ||||
| 404380.Gbem_0289 | (PF02754) | ||||
| 404380.Gbem_1643 | (PF04055) | ||||
| 404380.Gbem_1645 | (PF01715) | ||||
| 404380.Gbem_1883 | (PF03144) | ||||
| 404380.Gbem_1736 | (PF03063) | ||||
| 404380.Gbem_1469 | (PF01012) | ||||
| 404380.Gbem_1464 | (PF00549) | ||||
| 404380.Gbem_1465 | (PF00549) | ||||
| 404380.Gbem_1466 | (PF01012) | ||||
| 404380.Gbem_2241 | (PF01814) | ||||
| 404380.Gbem_2394 | (PF00989) | ||||
| 404380.Gbem_2391 | (PF04055) | ||||
| 404380.Gbem_2398 | (PF04055) | ||||
| 404380.Gbem_1250 | (PF13565) | ||||
| 404380.Gbem_0125 | (PF12838) | ||||
| 404380.Gbem_1655 | (PF04055) | ||||
| 404380.Gbem_3935 | (PF03144) | ||||
| 404380.Gbem_2838 | (PF02310) | ||||
| 404380.Gbem_1383 | (PF00989) | ||||
| 404380.Gbem_2121 | (PF00989) | ||||
| 404380.Gbem_2123 | (PF13281) | ||||
| 404380.Gbem_2340 | (PF02915) | ||||
| 404380.Gbem_2905 | (PF02754) | ||||
| 404380.Gbem_0626 | (PF01739) | ||||
| 404380.Gbem_0400 | (PF04055) | ||||
| 404380.Gbem_1043 | (PF01739) | ||||
| 404380.Gbem_1446 | (PF02754) | ||||
| 404380.Gbem_1447 | (PF12838) | ||||
| 404380.Gbem_2352 | (PF03144) | ||||
| 404380.Gbem_3192 | (PF13565) | ||||
| 404380.Gbem_2911 | (PF02754) | ||||
| 404380.Gbem_2914 | (PF02915) | ||||
| 404380.Gbem_0277 | (PF02310) | ||||
| 404380.Gbem_0474 | (PF03144) | ||||
| 404380.Gbem_0476 | (PF00989) | ||||
| 404380.Gbem_1451 | (PF12838) | ||||
| 404380.Gbem_2406 | (PF00989) | ||||
| 404380.Gbem_2030 | (PF01739) | ||||
| 404380.Gbem_2691 | (PF02310) | ||||
| 404380.Gbem_3180 | (PF02873) | ||||
| 404380.Gbem_0260 | (PF00549) | ||||
| 404380.Gbem_1595 | (PF01739) | ||||
| 404380.Gbem_1028 | (PF08392) | ||||
| 404380.Gbem_1333 | (PF01012) | ||||
| 404380.Gbem_2500 | (PF04055) | ||||
| 404380.Gbem_2379 | (PF01739) | ||||
| 404380.Gbem_3087 | (PF12838) | ||||
| 404380.Gbem_0072 | (PF03063) | ||||
| 404380.Gbem_3885 | (PF01058) | ||||
| 404380.Gbem_3883 | (PF12838) | ||||
| 404380.Gbem_1033 | (PF03063) | ||||
| 404380.Gbem_2562 | (PF01814) | ||||
| 404380.Gbem_2943 | (PF01739) | ||||
| 404380.Gbem_3560 | (PF02915) | ||||
| 404380.Gbem_0209 | (PF12838) | ||||
| 404380.Gbem_0660 | (PF13237) | ||||
| 404380.Gbem_0339 | (PF13565) | ||||
| 404380.Gbem_1952 | (PF00989) | ||||
| 404380.Gbem_1318 | (PF04055) | ||||
| 404380.Gbem_3143 | (PF00989) | ||||
| 404380.Gbem_2315 | (PF00025) | ||||
| 404380.Gbem_2313 | (PF02915) | ||||
| 404380.Gbem_2773 | (PF01814) | ||||
| 404380.Gbem_3139 | (PF01058) | ||||
| 404380.Gbem_3222 | (PF00549) | ||||
| 404380.Gbem_3223 | (PF00549) | ||||
| 404380.Gbem_0234 | (PF04055) | ||||
| 404380.Gbem_0235 | (PF04055) | ||||
| 404380.Gbem_0918 | (PF03144) | ||||
| 404380.Gbem_0178 | (PF01058) | ||||
| 404380.Gbem_0548 | (PF04055) | ||||
| 404380.Gbem_1303 | (PF13565) | ||||
| 404380.Gbem_3943 | (PF01739) | ||||
| 404380.Gbem_3233 | (PF03144) | ||||
| 404380.Gbem_2899 | (PF13187) | ||||
| 404380.Gbem_1978 | (PF12838) | ||||
| 404380.Gbem_2085 | (PF01012) | ||||
| 404380.Gbem_2083 | (PF04055) | ||||
| 404380.Gbem_2153 | (PF00989) | ||||
| 404380.Gbem_3938 | (PF02915) | ||||
| 404380.Gbem_2424 | (PF12899) | ||||
| 404380.Gbem_0146 | (PF01814) | ||||
| 404380.Gbem_0035 | (PF03144) | ||||
| 404380.Gbem_0030 | (PF12838) | ||||
| 404380.Gbem_0031 | (PF02754) | ||||
| 404380.Gbem_0032 | (PF13187) | ||||
| 404380.Gbem_4009 | (PF01814) | ||||
| 404380.Gbem_1786 | (PF04055) | ||||
| 404380.Gbem_0493 | (PF02873) | ||||
| 404380.Gbem_0761 | (PF04055) | ||||
| 404380.Gbem_0563 | (PF02754) | ||||
| 404380.Gbem_1141 | (PF00989) | ||||
| 404380.Gbem_1969 | (PF01058) | ||||
| 404380.Gbem_1369 | (PF01058) | ||||
| 404380.Gbem_1705 | (PF13565) | ||||
| 404380.Gbem_1219 | (PF13565) | ||||
| 404380.Gbem_3325 | (PF02915) | ||||
| 404380.Gbem_3925 | (PF01058) | ||||
| 404380.Gbem_2458 | (PF12038) | ||||
| 404380.Gbem_3920 | (PF12838) | ||||
| 404380.Gbem_2456 | (PF04055) | ||||
| 404380.Gbem_3454 | (PF05140) | ||||
| 404380.Gbem_3100 | (PF04055) | ||||
| 404380.Gbem_0158 | (PF04055) | ||||
| 404380.Gbem_0807 | (PF04055) | ||||
| 404380.Gbem_0979 | (PF01715) | ||||
| 404380.Gbem_0975 | (PF00989) |
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
- 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: NO (FDR = 7.2 %)
- Functional Type VI secretion system: YES (FDR = 7.7 %)
Estimated copy number = 0.375 (3/8 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 = 0.375 (3/8 KEGG proteins)
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