Effective results for Sphingobium japonicum UT26S (eggnog40)

Summary

Number of putative secreted proteins: 78
- Predicted by T4SEpre: 56
- Predicted by EffectiveELD: 8 eukaryotic-like domains, contained in 30 proteins (0 high, 30 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
452662.SJA_C1-08070			+		mitochondrial
452662.SJA_C2-01790			+		(ER); (mitochondrial)
452662.SJA_C1-00260				(PF02195)	(ER)
452662.SJA_C1-21120			+		ER; (ER)
452662.SJA_C1-21840			+		ER
452662.SJA_C2-05460			+		ER
452662.SJA_C1-13340				(PF06455)	ER
452662.SJA_C1-14350				(PF01541)	mitochondrial; (mitochondrial)
452662.SJA_C1-22430			+		(ER)
452662.SJA_C1-29260				(PF01541)	mitochondrial
452662.SJA_C1-25340			+		ER
452662.SJA_C1-26840			+		(mitochondrial)
452662.SJA_C2-03680				(PF07110)	(mitochondrial); mitochondrial
452662.SJA_C1-13540			+		(mitochondrial)
452662.SJA_C1-12890			+		(mitochondrial)
452662.SJA_C1-14020			+		ER
452662.SJA_C2-04730				(PF02195)	(mitochondrial)
452662.SJA_C1-04920			+		(ER)
452662.SJA_C1-33770				(PF02933)	(ER)
452662.SJA_C1-09880			+		(mitochondrial)
452662.SJA_C1-34680			+		(mitochondrial)
452662.SJA_C1-04450			+		(plastid)
452662.SJA_C1-34550				(PF01541)	(mitochondrial)
452662.SJA_C1-10950			+		(ER)
452662.SJA_C1-33230				(PF01541)	(mitochondrial)
452662.SJA_C1-15490			+
452662.SJA_C1-22600				(PF01541)
452662.SJA_C1-10050			+
452662.SJA_C1-20280				(PF02195)
452662.SJA_C1-29360			+
452662.SJA_C1-21480			+
452662.SJA_C1-01500			+
452662.SJA_C2-03980			+
452662.SJA_C1-34460			+
452662.SJA_C1-06290			+
452662.SJA_C1-24860			+
452662.SJA_C1-27340			+
452662.SJA_C1-29530				(PF03031)
452662.SJA_C1-31760			+
452662.SJA_C1-22610			+
452662.SJA_C1-26090				(PF02195)
452662.SJA_C2-04280			+
452662.SJA_C2-04350			+
452662.SJA_C1-04400				(PF02195)
452662.SJA_C1-03540				(PF02195)
452662.SJA_C1-28590			+
452662.SJA_C1-14360			+
452662.SJA_C2-05890				(PF02195)
452662.SJA_C1-29880				(PF02195)
452662.SJA_C1-33850			+
452662.SJA_C1-32850			+
452662.SJA_C1-17140				(PF01541)
452662.SJA_C1-25960			+
452662.SJA_C1-25560			+
452662.SJA_C1-16810			+
452662.SJA_C1-09770			+
452662.SJA_C1-20100			+
452662.SJA_C2-04740			+
452662.SJA_C1-34510			+
452662.SJA_C1-01000				(PF01541)
452662.SJA_C1-05580				(PF07110)
452662.SJA_C1-05310				(PF03332)
452662.SJA_C1-32250			+
452662.SJA_C1-24300				(PF01541)
452662.SJA_C1-28340			+
452662.SJA_C1-33070				(PF03332)
452662.SJA_C1-05540				(PF07110)
452662.SJA_C2-04460				(PF02195)
452662.SJA_C1-32620				(PF16715)
452662.SJA_C1-01670			+
452662.SJA_C1-32530			+
452662.SJA_C1-05800			+
452662.SJA_C1-04560			+
452662.SJA_C2-00170				(PF02195)
452662.SJA_C1-18380				(PF02195)
452662.SJA_C1-10730			+
452662.SJA_C1-31880				(PF02195)
452662.SJA_C1-21810				(PF01541)

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 = 2.0 (20/10 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=
==========================================================