Effective results for Helicobacter bizzozeronii CIII-1 (eggnog40)

Summary

Number of putative secreted proteins: 109
- Predicted by T4SEpre: 70
- Predicted by EffectiveELD: 14 eukaryotic-like domains, contained in 57 proteins (0 high, 57 medium Z-score)
Predicted protein secretion systems (parentheses indicate weak positive predictions lacking more than 50% of core proteins of a secretion system): Type IV, (Type VI)

Protein based results

Putative secreted proteins (weak evidence indicated by parentheses)

Protein	EffectiveT3	EffectiveCCBD	T4SEpre	EffectiveELD	Predotar
1002804.HBZC1_01480			+		ER
1002804.HBZC1_12630			+		ER
1002804.HBZC1_05130			+		ER
1002804.HBZC1_10750				(PF03382)	(mitochondrial)
1002804.HBZC1_09810			+		(mitochondrial)
1002804.HBZC1_18370			+		ER
1002804.HBZC1_04860				(PF02844) (PF02843)	(mitochondrial)
1002804.HBZC1_03660				(PF01535)	(ER)
1002804.HBZC1_07230				(PF08238)	ER
1002804.HBZC1_03200			+		ER
1002804.HBZC1_07220				(PF08238)	ER
1002804.HBZC1_04790				(PF01755)	mitochondrial
1002804.HBZC1_00120				(PF08238)	ER
1002804.HBZC1_01190			+		ER
1002804.HBZC1_06690				(PF08238)	ER
1002804.HBZC1_08270			+		(ER)
1002804.HBZC1_00910				(PF08238)	ER
1002804.HBZC1_15640				(PF02844)	(mitochondrial)
1002804.HBZC1_06170			+		ER
1002804.HBZC1_02430				(PF08238)	ER
1002804.HBZC1_15650				(PF02843)	ER; (ER)
1002804.HBZC1_03870			+		ER
1002804.HBZC1_10540			+		ER
1002804.HBZC1_15250				(PF08238)	ER
1002804.HBZC1_00900				(PF08238)	ER
1002804.HBZC1_09700				(PF08238)	ER
1002804.HBZC1_10030				(PF11074)	mitochondrial; (mitochondrial)
1002804.HBZC1_11140				(PF08238)	ER
1002804.HBZC1_10370			+		ER
1002804.HBZC1_17360			+	(PF03235)
1002804.HBZC1_01280			+		(mitochondrial)
1002804.HBZC1_09910			+		(mitochondrial)
1002804.HBZC1_04010			+		(plastid)
1002804.HBZC1_17310			+		(mitochondrial)
1002804.HBZC1_10760				(PF03235)	(plastid)
1002804.HBZC1_04950				(PF04998) (PF00562)
1002804.HBZC1_09590			+
1002804.HBZC1_17190			+
1002804.HBZC1_04940				(PF04998)
1002804.HBZC1_04830				(PF13507)
1002804.HBZC1_10010				(PF08238)
1002804.HBZC1_08430				(PF03235)
1002804.HBZC1_16420				(PF08238)
1002804.HBZC1_15770			+
1002804.HBZC1_07880				(PF08238)
1002804.HBZC1_04840				(PF13507)
1002804.HBZC1_17160			+
1002804.HBZC1_15500				(PF03382)
1002804.HBZC1_18050			+
1002804.HBZC1_15720				(PF01687)
1002804.HBZC1_02900				(PF01555)
1002804.HBZC1_08610				(PF03382)
1002804.HBZC1_07980				(PF03235)
1002804.HBZC1_15490				(PF03382)
1002804.HBZC1_16620				(PF01555)
1002804.HBZC1_15710				(PF01687)
1002804.HBZC1_01980				(PF03382)
1002804.HBZC1_17020				(PF01142)
1002804.HBZC1_08970				(PF01555)
1002804.HBZC1_14120			+
1002804.HBZC1_17380				(PF03235)
1002804.HBZC1_14380				(PF01555)
1002804.HBZC1_01410				(PF01555)
1002804.HBZC1_02940			+
1002804.HBZC1_11710			+
1002804.HBZC1_14570			+
1002804.HBZC1_00890				(PF08238)
1002804.HBZC1_03780			+
1002804.HBZC1_05880			+
1002804.HBZC1_04930				(PF03382)
1002804.HBZC1_08200			+
1002804.HBZC1_07030			+
1002804.HBZC1_00050			+
1002804.HBZC1_06300			+
1002804.HBZC1_01740			+
1002804.HBZC1_04210			+
1002804.HBZC1_12100				(PF01555)
1002804.HBZC1_04770				(PF01755)
1002804.HBZC1_08860			+
1002804.HBZC1_18470				(PF01555)
1002804.HBZC1_04000			+
1002804.HBZC1_09310			+
1002804.HBZC1_09980			+
1002804.HBZC1_00690			+
1002804.HBZC1_11950			+
1002804.HBZC1_00260				(PF01142)
1002804.HBZC1_15480				(PF03382)
1002804.HBZC1_16260			+
1002804.HBZC1_17130			+
1002804.HBZC1_09990			+
1002804.HBZC1_06120			+
1002804.HBZC1_15920				(PF01555)
1002804.HBZC1_00270				(PF01142)
1002804.HBZC1_10310			+
1002804.HBZC1_15470			+
1002804.HBZC1_16410				(PF08238)
1002804.HBZC1_09670			+
1002804.HBZC1_08650				(PF03235)
1002804.HBZC1_17120			+
1002804.HBZC1_07460				(PF01755)
1002804.HBZC1_04960				(PF00562)
1002804.HBZC1_01700			+
1002804.HBZC1_07600				(PF03382)
1002804.HBZC1_16400				(PF03235)
1002804.HBZC1_00730			+
1002804.HBZC1_01290			+
1002804.HBZC1_02380			+
1002804.HBZC1_08390			+
1002804.HBZC1_03130				(PF01142)

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

• T4SEpre bpbAac predictions (T4SEpre_bpbAac_FinalResult.csv)
• T4SEpre psAac predictions (T4SEpre_psAac_FinalResult.csv)
• 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: YES (FDR = 7.2 %)
  Estimated copy number = 0.8 (8/10 KEGG proteins)
• Functional Type VI secretion system: YES (FDR = 7.7 %)
  Estimated copy number = 0.25 (2/8 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=
==========================================================