UHM_Koxytoca — NovInvenio reports

Lineage-specific gene analysis · one folder, three interactive reports

Reports

Each page is self-contained — open it directly, no network needed.

Novelty candidatesLineage-specific genes: present across the ingroup, absent from every outgroup proteome. Core genesNear-universally conserved genes shared by essentially every proteome, ingroup and outgroup. Candidate gene lossesGene families conserved across the outgroups but (nearly) absent from the ingroup. Functional enrichment (novelty)Pfam term enrichment of the novelty candidates against the proteome background. InterPro and GO: not available. Functional enrichment (loss)Pfam term enrichment of the loss candidates against the proteome background. InterPro and GO: not available.

Run summary

Parameters and proteomes from config.csv.

Ingroup proteomes
18
Outgroup proteomes
16
Search tool
diamond
Ingroup min fraction
0.75
Outgroup min fraction
0.75
Loss ingroup max fraction
0
Core min fraction
0.95

Ingroup (18)

Genes are called lineage-specific relative to this clade.

ShortSpeciesTaxon group
UHM102bin47Klebsiella oxytoca UHM102bin47UHM_koxytoca
UHM125bin22Klebsiella oxytoca UHM125bin22UHM_koxytoca
UHM125bin48Klebsiella oxytoca UHM125bin48UHM_koxytoca
UHM145bin17Klebsiella oxytoca UHM145bin17UHM_koxytoca
UHM145bin33Klebsiella oxytoca UHM145bin33UHM_koxytoca
UHM145bin28Klebsiella oxytoca UHM145bin28UHM_koxytoca
UHM17bin35Klebsiella oxytoca UHM17bin35UHM_koxytoca
UHM18bin40Klebsiella oxytoca UHM18bin40UHM_koxytoca
UHM20bin40Klebsiella oxytoca UHM20bin40UHM_koxytoca
UHM20bin12Klebsiella oxytoca UHM20bin12UHM_koxytoca
UHM22bin50Klebsiella oxytoca UHM22bin50UHM_koxytoca
UHM22bin54Klebsiella oxytoca UHM22bin54UHM_koxytoca
UHM22bin8Klebsiella oxytoca UHM22bin8UHM_koxytoca
UHM40bin4Klebsiella oxytoca UHM40bin4UHM_koxytoca
UHM40bin27Klebsiella oxytoca UHM40bin27UHM_koxytoca
UHM43bin53Klebsiella oxytoca UHM43bin53UHM_koxytoca
UHM56bin19Klebsiella oxytoca UHM56bin19UHM_koxytoca
UHM72bin19Klebsiella oxytoca UHM72bin19UHM_koxytoca

Outgroup (16)

Background proteomes used to exclude broadly conserved genes.

ShortSpeciesTaxon group
KoxO_050916275Klebsiella oxytoca KOHN1Mammal_koxytoca
KoxO_017310465Klebsiella oxytoca IR5392Mammal_koxytoca
KoxO_929608445Klebsiella oxytoca cpe088Mammal_koxytoca
KoxO_040561445Klebsiella oxytoca ST106KO11Mammal_koxytoca
KoxO_900083795Klebsiella oxytoca 2880STDY5682743Mammal_koxytoca
KoxO_024918735Klebsiella oxytoca ST34Mammal_koxytoca
KoxO_902162875Klebsiella oxytoca 4928STDY7071180Mammal_koxytoca
KoxO_053276915Klebsiella oxytoca KP111Mammal_koxytoca
KoxO_030343105Klebsiella oxytoca NMI1636_19Mammal_koxytoca
KoxO_030343375Klebsiella oxytoca NMI2383_18Mammal_koxytoca
KoxO_016734995Klebsiella oxytoca KLEB012Mammal_koxytoca
KoxO_030343565Klebsiella oxytoca NMI4062_17Mammal_koxytoca
KoxO_900083995Klebsiella oxytoca 2880STDY5682534Mammal_koxytoca
KoxO_004360035Klebsiella oxytoca SO-KOX16-1Mammal_koxytoca
KoxO_030344075Klebsiella oxytoca NMI4566_15Mammal_koxytoca
KoxO_051951865Klebsiella oxytoca KO67Mammal_koxytoca