Effective results for Leptothrix cholodnii SP-6 (eggnog40)

Summary

Number of putative secreted proteins: 60
- Predicted by T4SEpre: 0
- Predicted by EffectiveELD: 18 eukaryotic-like domains, contained in 60 proteins (1 high, 59 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
395495.Lcho_0048				(PF02630)	ER
395495.Lcho_3829				(PF02630)	(ER)
395495.Lcho_3941				(PF00909)	ER
395495.Lcho_2540				(PF01012)	(mitochondrial); mitochondrial
395495.Lcho_1450				(PF02239)	ER
395495.Lcho_0857				(PF01012)	(mitochondrial); mitochondrial
395495.Lcho_0070				(PF02630)	(mitochondrial)
395495.Lcho_3791				(PF02630)	(mitochondrial)
395495.Lcho_1194				(PF01012)	(mitochondrial); mitochondrial
395495.Lcho_1444				(PF02239)	ER
395495.Lcho_1442				(PF02239)	ER
395495.Lcho_1995				(PF02630)	ER
395495.Lcho_4373				(PF00909)	mitochondrial; (mitochondrial)
395495.Lcho_3598				(PF01012)	(mitochondrial); mitochondrial
395495.Lcho_1386				(PF13480)	mitochondrial
395495.Lcho_0650				(PF02630)	ER
395495.Lcho_2647				(PF00909)	ER
395495.Lcho_3891				(PF02630)	ER
395495.Lcho_3892				(PF02239)	ER
395495.Lcho_0663				(PF00909)	ER
395495.Lcho_0157				(PF00909)	ER
395495.Lcho_0313				(PF00925) (PF12471)
395495.Lcho_2720				(PF13480)	(ER)
395495.Lcho_0858				(PF00766) (PF01012)
395495.Lcho_1195				(PF00766) (PF01012)
395495.Lcho_3599				(PF00766) (PF01012)
395495.Lcho_2539				(PF00766) (PF01012)
395495.Lcho_1369				(PF00766) (PF01012)
395495.Lcho_3890				(PF02630)	(ER)
395495.Lcho_0163				(PF00766) (PF01012)
395495.Lcho_0162				(PF01012)	(mitochondrial)
395495.Lcho_2627				(PF02630)
395495.Lcho_2489				(PF00925)
395495.Lcho_4303				(PF09298)
395495.Lcho_1179				(PF13480)
395495.Lcho_0314				(PF07958)
395495.Lcho_2793				(PF05706)
395495.Lcho_0432				(PF09298)
395495.Lcho_2360				(PF13480)
395495.Lcho_1452				(PF13429)
395495.Lcho_0855				(PF00925)
395495.Lcho_2996				(PF12513)
395495.Lcho_1192				(PF05187)
395495.Lcho_2161				(PF00925)
395495.Lcho_0017				(PF13429)
395495.Lcho_0709				(PF09298)
395495.Lcho_2257				PF16190
395495.Lcho_1251				(PF10013)	not used
395495.Lcho_3113				(PF02239)
395495.Lcho_2069				(PF05187)
395495.Lcho_1399				(PF13480)
395495.Lcho_2044				(PF09298)
395495.Lcho_3657				(PF16155)
395495.Lcho_1368				(PF01012)
395495.Lcho_2935				(PF00925)
395495.Lcho_1371				(PF05187)
395495.Lcho_0158				(PF05187)
395495.Lcho_0571				(PF13281)
395495.Lcho_3070				(PF13480)
395495.Lcho_3071				(PF13480)

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 = 3.0 (24/8 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=
==========================================================