Effective results for Shewanella loihica PV-4 (eggnog40)

Summary

Number of putative secreted proteins: 37
- Predicted by T4SEpre: 0
- Predicted by EffectiveELD: 11 eukaryotic-like domains, contained in 37 proteins (1 high, 36 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)

ProteinEffectiveT3EffectiveCCBDT4SEpreEffectiveELDPredotar
323850.Shew_2246(PF00849)(mitochondrial)
323850.Shew_0807(PF02225)ER
323850.Shew_0935(PF02225)ER
323850.Shew_1510(PF02225)ER
323850.Shew_2529(PF00849)ER; (ER)
323850.Shew_2208(PF02225)ER
323850.Shew_2051(PF09317)ER
323850.Shew_0781(PF02225)ER; (ER)
323850.Shew_3152(PF02225)ER; (ER)
323850.Shew_2367(PF04970)ER
323850.Shew_2960(PF02225)ER
323850.Shew_3180(PF00849)mitochondrial
323850.Shew_2108(PF09317)ER
323850.Shew_2720(PF02225)ER
323850.Shew_3418(PF06468)ER
323850.Shew_3417(PF06468)mitochondrial
323850.Shew_1678(PF07766)mitochondrial
323850.Shew_0916(PF00849)(mitochondrial)
323850.Shew_1562(PF00849)plastid
323850.Shew_1028(PF14216)
323850.Shew_1253(PF04970)
323850.Shew_0814(PF00849)
323850.Shew_1620PF01536
323850.Shew_2643(PF00849)
323850.Shew_2975(PF00849)
323850.Shew_2443(PF02225)
323850.Shew_3003(PF09317)
323850.Shew_2996(PF00026)
323850.Shew_2547(PF00849)
323850.Shew_0783(PF00849)
323850.Shew_2950(PF00849)
323850.Shew_0099(PF00849)
323850.Shew_1594(PF00849)
323850.Shew_3348(PF00849)
323850.Shew_1460(PF00849)
323850.Shew_0508(PF16983)
323850.Shew_1642(PF05548)

Detailed merged results for each protein sequence

Individual results for each protein sequence

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 = 0.625 (5/8 KEGG proteins)

Individual results for each secretion system

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