Effective results for Shewanella violacea DSS12 (eggnog40)

Summary

Number of putative secreted proteins: 63
- Predicted by T4SEpre: 0
- Predicted by EffectiveELD: 25 eukaryotic-like domains, contained in 63 proteins (3 high, 60 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
637905.SVI_1093				(PF13582) (PF00801)	ER
637905.SVI_1094				(PF05572) (PF00801)	ER; (ER)
637905.SVI_2644				(PF00801)	ER
637905.SVI_0874				(PF00801)	ER
637905.SVI_3085				(PF07766)	mitochondrial
637905.SVI_0833				(PF14312)	ER
637905.SVI_2320				(PF09317)	ER
637905.SVI_1964				(PF05023)	ER
637905.SVI_2434				(PF05572)	ER
637905.SVI_0876				(PF00801)	ER
637905.SVI_3114				(PF09619)	ER
637905.SVI_2427				(PF06041)	(ER); ER
637905.SVI_4266				(PF00031)	ER
637905.SVI_3108				(PF09619)	ER
637905.SVI_3906				(PF06468)	mitochondrial; (mitochondrial)
637905.SVI_3905				(PF06468)	ER
637905.SVI_2272				(PF09619)	ER
637905.SVI_2381				(PF09317)	ER
637905.SVI_3757				(PF00849)	mitochondrial
637905.SVI_2441				(PF00305) PF00168
637905.SVI_1856				(PF02460)	(mitochondrial)
637905.SVI_0677				(PF06041)	(mitochondrial)
637905.SVI_2101				(PF13391)	(mitochondrial)
637905.SVI_1922				(PF00801) (PF05572)
637905.SVI_0871				(PF00801)	ER
637905.SVI_1570				(PF00849)	(ER)
637905.SVI_2887				(PF13391)	(mitochondrial)
637905.SVI_3488				(PF03199) (PF03917)
637905.SVI_3719				(PF00801)	(mitochondrial)
637905.SVI_1669				PF08030 (PF08022)
637905.SVI_1052				(PF06041)
637905.SVI_2652				(PF13495)
637905.SVI_3526				(PF14312)
637905.SVI_1840				(PF08487)
637905.SVI_2647				(PF13495)
637905.SVI_0072				(PF01218)	not used
637905.SVI_0071				(PF01218)	not used
637905.SVI_0070				(PF01218)
637905.SVI_1823				(PF00849)
637905.SVI_4237				(PF00849)
637905.SVI_1318				(PF09317)
637905.SVI_2114				(PF08487)
637905.SVI_3569				(PF00849)
637905.SVI_1155				(PF03945)
637905.SVI_0822				(PF00849)
637905.SVI_2797				(PF00849)
637905.SVI_3426				(PF00849)
637905.SVI_3431				(PF00849)
637905.SVI_3127				(PF00849)
637905.SVI_1681				(PF13495)
637905.SVI_1195				(PF13495)
637905.SVI_1224				(PF00849)
637905.SVI_2554				(PF00849)
637905.SVI_3591				(PF00849)
637905.SVI_4260				(PF00801)
637905.SVI_2132				(PF00849)
637905.SVI_2524				PF01536
637905.SVI_3210				(PF00849)
637905.SVI_3923				(PF08022)
637905.SVI_2502				(PF13495)
637905.SVI_1396				(PF13391)
637905.SVI_3651				(PF00849)
637905.SVI_3039				(PF00849)

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 = 0.75 (6/8 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=
==========================================================