Effective results for Psychromonas ingrahamii 37 (eggnog40)

Summary

Number of putative secreted proteins: 46
- Predicted by T4SEpre: 0
- Predicted by EffectiveELD: 24 eukaryotic-like domains, contained in 46 proteins (13 high, 33 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
357804.Ping_3250				PF11999	ER
357804.Ping_3251				PF11999	ER
357804.Ping_1782				PF11999	(ER)
357804.Ping_3248				PF11999	ER
357804.Ping_1164				(PF13936)	(mitochondrial)
357804.Ping_2538				(PF08495) (PF10442)	(mitochondrial)
357804.Ping_1550				(PF10013)	(mitochondrial)
357804.Ping_2613				(PF00163)	(mitochondrial)
357804.Ping_3153				(PF02010)	ER
357804.Ping_2599				(PF13936)	(mitochondrial)
357804.Ping_1485				(PF13936)	(mitochondrial)
357804.Ping_0848				PF11999	(ER)
357804.Ping_3500				(PF00163)	(mitochondrial)
357804.Ping_1815				(PF13936)	(mitochondrial)
357804.Ping_2652				(PF13936)	(mitochondrial)
357804.Ping_2317				PF11999	(ER)
357804.Ping_3499				(PF01000) (PF01193)
357804.Ping_2699				(PF13551) (PF13592)
357804.Ping_1345				(PF13551) (PF13592)
357804.Ping_0002				(PF13551) (PF13592)
357804.Ping_1360				(PF13551) (PF13592)
357804.Ping_1512				(PF13551) (PF13592)
357804.Ping_0141				(PF13936)	(mitochondrial)
357804.Ping_2614				(PF01000) (PF01193)
357804.Ping_3194				(PF13551) (PF13592)
357804.Ping_1203				(PF08495) (PF10442)
357804.Ping_1202				(PF08495) (PF10442)
357804.Ping_1204				(PF08495) (PF10442)
357804.Ping_1530				(PF09996)
357804.Ping_3498				(PF01196)
357804.Ping_1527				(PF09996)
357804.Ping_2850				PF11999
357804.Ping_1294				(PF10354)
357804.Ping_0374				PF01536
357804.Ping_1818				PF03366
357804.Ping_0634				(PF13875)
357804.Ping_3638				(PF05706)
357804.Ping_1247				(PF02933)
357804.Ping_2612				PF00411
357804.Ping_2611				PF00416
357804.Ping_2615				(PF01196)
357804.Ping_3395				(PF01786)
357804.Ping_1954				(PF14701)
357804.Ping_3501				PF00411
357804.Ping_3502				PF00416
357804.Ping_1733				(PF03522)

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 = 1.375 (11/8 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=
==========================================================