Effective results for Hyphomicrobium denitrificans ATCC 51888 (eggnog40)

Summary

Number of putative secreted proteins: 119
- Predicted by T4SEpre: 115
- Predicted by EffectiveELD: 10 eukaryotic-like domains, contained in 27 proteins (7 high, 20 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)

Protein based results

Putative secreted proteins (weak evidence indicated by parentheses)

Protein	EffectiveT3	EffectiveCCBD	T4SEpre	EffectiveELD	Predotar
582899.Hden_1762			+		ER
582899.Hden_2016			+		(mitochondrial); plastid
582899.Hden_3051				(PF13506)	ER
582899.Hden_2942			+		ER
582899.Hden_2837			+		(ER)
582899.Hden_2834			+		ER
582899.Hden_1375			+		ER
582899.Hden_2101			+		ER
582899.Hden_3444			+		ER
582899.Hden_3447			+		ER
582899.Hden_0484			+		ER; (plastid)
582899.Hden_0483				(PF13506)	ER
582899.Hden_1603			+		(mitochondrial); (plastid)
582899.Hden_1000			+		ER
582899.Hden_3090			+		ER
582899.Hden_2870			+		(ER)
582899.Hden_0829				(PF00856)	mitochondrial
582899.Hden_3402			+		(mitochondrial)
582899.Hden_1068			+		mitochondrial; (mitochondrial)
582899.Hden_2090			+		mitochondrial; (mitochondrial)
582899.Hden_1075			+		ER; (ER)
582899.Hden_1315			+		ER
582899.Hden_1425			+		mitochondrial
582899.Hden_2795				(PF00856)	mitochondrial
582899.Hden_1449			+		ER
582899.Hden_2119			+		ER
582899.Hden_3333			+		ER
582899.Hden_2335			+		ER
582899.Hden_2889			+		ER
582899.Hden_0491			+		ER
582899.Hden_0272			+		ER
582899.Hden_2179			+		ER
582899.Hden_0866			+		ER; (ER)
582899.Hden_0314			+		(mitochondrial)
582899.Hden_2132			+		ER
582899.Hden_0488				(PF13506)	ER
582899.Hden_3343			+		ER
582899.Hden_3341			+		ER
582899.Hden_1878			+		ER
582899.Hden_1402			+		ER
582899.Hden_2448			+		ER
582899.Hden_1156			+		ER
582899.Hden_3146			+		mitochondrial
582899.Hden_0545			+		ER
582899.Hden_1418			+		ER
582899.Hden_1596				PF13392 PF00847
582899.Hden_0177				PF13392 PF00847
582899.Hden_2685			+		(ER)
582899.Hden_1322			+		(plastid)
582899.Hden_0249			+		(mitochondrial)
582899.Hden_2406			+		(ER)
582899.Hden_1457			+		(ER)
582899.Hden_0109				PF13392 PF00847
582899.Hden_2564			+		ER
582899.Hden_1886			+		(ER)
582899.Hden_1529				PF13392 PF00847
582899.Hden_0386				(PF06258)
582899.Hden_0141				(PF02357)
582899.Hden_3538			+
582899.Hden_0154			+
582899.Hden_2487			+
582899.Hden_1561				(PF02357)
582899.Hden_1366			+
582899.Hden_1587				PF13392
582899.Hden_1997			+
582899.Hden_0168				PF13392
582899.Hden_1573			+
582899.Hden_3513			+
582899.Hden_3084			+
582899.Hden_0204			+
582899.Hden_1005				(PF02357)
582899.Hden_1001				(PF04519)
582899.Hden_0949			+
582899.Hden_1837			+
582899.Hden_0235			+
582899.Hden_3113			+
582899.Hden_1010			+
582899.Hden_2476			+
582899.Hden_0147				PF13392
582899.Hden_1244			+
582899.Hden_2046			+
582899.Hden_0828				(PF00856)
582899.Hden_2688			+
582899.Hden_0355			+
582899.Hden_3310			+
582899.Hden_1809				(PF06258)
582899.Hden_3138			+
582899.Hden_1494				(PF04519)
582899.Hden_2789				(PF04519)
582899.Hden_0328			+
582899.Hden_0784			+
582899.Hden_0255				(PF12576)
582899.Hden_2523			+
582899.Hden_0806			+
582899.Hden_2661			+
582899.Hden_0361			+
582899.Hden_2081			+
582899.Hden_2240			+
582899.Hden_3330				(PF02689)
582899.Hden_1040			+
582899.Hden_2533			+
582899.Hden_0776			+
582899.Hden_3357			+
582899.Hden_2350			+
582899.Hden_1219			+
582899.Hden_2513			+
582899.Hden_2342			+
582899.Hden_0850				(PF05185)
582899.Hden_1267			+
582899.Hden_2365				(PF04519)
582899.Hden_3161			+
582899.Hden_1228			+
582899.Hden_2611			+
582899.Hden_0942			+
582899.Hden_2149			+
582899.Hden_2389				(PF04519)
582899.Hden_0437				(PF02357)
582899.Hden_0951			+
582899.Hden_0559			+

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 = 0.0 (0/10 KEGG proteins)
• Functional Type VI secretion system: NO (FDR = 7.7 %)

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=
==========================================================