Effective results for Shewanella woodyi ATCC 51908 (eggnog40)

Summary

Number of putative secreted proteins: 104
- Predicted by T4SEpre: 0
- Predicted by EffectiveELD: 30 eukaryotic-like domains, contained in 104 proteins (5 high, 99 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
392500.Swoo_3885				(PF01773) (PF07662)	ER
392500.Swoo_2675				(PF01773) (PF07662)	ER
392500.Swoo_3189				(PF01773) (PF07662)	ER
392500.Swoo_3041				(PF05922) (PF02225)	ER
392500.Swoo_1394				(PF05922) (PF02225)	ER; (ER)
392500.Swoo_4915				(PF01773) (PF07662)	ER
392500.Swoo_1500				(PF05922) (PF02225)	ER
392500.Swoo_3915				(PF00629) (PF00801)	ER
392500.Swoo_3551				(PF01773) (PF07662)	ER
392500.Swoo_2666				(PF05922)	ER
392500.Swoo_0968				(PF01346)	ER
392500.Swoo_3431				(PF02225)	ER
392500.Swoo_1102				(PF01346)	ER
392500.Swoo_2470				(PF09619)	ER
392500.Swoo_0647				(PF00801)	ER; (ER)
392500.Swoo_3193				(PF00326)	ER
392500.Swoo_1349				(PF00245)	ER
392500.Swoo_1126				(PF00326)	ER
392500.Swoo_1911				(PF00801)	ER
392500.Swoo_1350				(PF00245)	(ER); ER
392500.Swoo_0393				(PF00326)	ER
392500.Swoo_2392				(PF13436)	ER
392500.Swoo_4159				(PF00326)	ER
392500.Swoo_0529				(PF00326)	ER
392500.Swoo_3465				(PF00326)	ER
392500.Swoo_0844				(PF00326)	ER
392500.Swoo_2604				(PF09317)	ER
392500.Swoo_4565				(PF00326)	ER
392500.Swoo_0115				(PF00801)	(ER); ER
392500.Swoo_2286				(PF10142)	ER
392500.Swoo_2359				(PF05922)	ER
392500.Swoo_4827				(PF00801)	(ER); (mitochondrial)
392500.Swoo_0291				(PF06468)	ER
392500.Swoo_4763				(PF00326)	ER
392500.Swoo_3243				(PF00326)	ER
392500.Swoo_2996				(PF00883)	(mitochondrial)
392500.Swoo_2373				(PF05922)	ER
392500.Swoo_3767				(PF02225)	(ER)
392500.Swoo_3768				(PF02225) (PF02010)	(ER)
392500.Swoo_3769				(PF00326)	ER
392500.Swoo_4648				(PF00801)	ER
392500.Swoo_4483				(PF00326)	ER
392500.Swoo_2228				(PF00326)	ER
392500.Swoo_4136				(PF00245)	ER
392500.Swoo_2542				(PF09317)	ER
392500.Swoo_4261				(PF00326)	ER
392500.Swoo_2940				(PF00326)	ER
392500.Swoo_4490				(PF00326)	ER
392500.Swoo_3209				(PF09619)	ER
392500.Swoo_3205				(PF09619)	ER
392500.Swoo_1207				(PF00245)	mitochondrial
392500.Swoo_1208				(PF00326)	ER
392500.Swoo_0557				(PF00801)	ER
392500.Swoo_3941				PF14845	ER
392500.Swoo_4518				(PF00326)	ER
392500.Swoo_4475				(PF01346)	ER
392500.Swoo_4454				(PF01346)	(ER)
392500.Swoo_3188				(PF00883)	(plastid)
392500.Swoo_3429				(PF00629) (PF00801)
392500.Swoo_2736				(PF00326)	(ER)
392500.Swoo_0211				(PF13816)	(mitochondrial)
392500.Swoo_2747				(PF02225)	(mitochondrial)
392500.Swoo_2953				(PF00801)	(plastid)
392500.Swoo_2096				(PF03199) (PF03917)
392500.Swoo_2919				PF00305
392500.Swoo_4445				(PF08022)
392500.Swoo_2058				PF01536
392500.Swoo_1556				(PF14027)
392500.Swoo_0572				(PF00849)
392500.Swoo_2907				(PF00849)
392500.Swoo_3602				(PF00883)
392500.Swoo_3670				(PF08014)
392500.Swoo_0652				(PF10509)
392500.Swoo_3722				(PF00849)
392500.Swoo_3289				(PF00849)
392500.Swoo_1751				(PF00849)
392500.Swoo_2703				(PF00849)
392500.Swoo_3873				(PF00849)
392500.Swoo_4379				(PF00332)
392500.Swoo_4415				(PF07720)
392500.Swoo_2380				(PF00849)
392500.Swoo_4380				(PF00332)
392500.Swoo_3730				(PF00849)
392500.Swoo_2033				(PF00849)
392500.Swoo_1076				(PF00883)
392500.Swoo_0913				(PF00849)
392500.Swoo_0915				(PF08014)
392500.Swoo_0917				(PF00849)
392500.Swoo_0598				(PF16983)
392500.Swoo_3580				(PF01346)
392500.Swoo_1504				(PF09317)
392500.Swoo_0582				(PF06468)
392500.Swoo_2085				(PF10509)
392500.Swoo_1049				(PF00849)
392500.Swoo_2318				PF00305
392500.Swoo_3662				(PF10509)
392500.Swoo_4781				(PF00849)
392500.Swoo_3796				(PF00883)
392500.Swoo_2449				(PF14027)
392500.Swoo_3153				(PF00849)
392500.Swoo_0942				(PF00849)
392500.Swoo_3411				(PF00849)
392500.Swoo_3415				PF00305
392500.Swoo_3638				(PF08022)

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 = 1.875 (15/8 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=
==========================================================