Ubiquitin System — Tree (Apium graveolens)

Ubiquitin System (Apium graveolens)

Method. Proteins were annotated using UUCD-derived HMM profiles and family-specific score cutoffs with HMMER (hmmsearch).

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+DUB(47 genes, 4 categories)
- +JAMM(3 genes)
- +UCH(1 genes)
  - Ag2G01222
- +ULP(7 genes)
- +USP(36 genes)
+E1(10 genes)
+E2(55 genes, 2 categories)
- +UBC(49 genes)
- +UEV(6 genes)
+E3_activity(574 genes, 4 categories)
+E3_adaptor(608 genes, 1 categories)
- +Cullin_RING(608 genes, 5 categories)
+UBD(171 genes, 4 categories)
- +Alpha-Helix(36 genes, 3 categories)
  - +CUE(2 genes)
    - Ag4G01643
    - Ag6G01700
  - +UBA(28 genes)
  - +UIM(6 genes)
- +Beta-Prp(91 genes)
- +UBC-like(43 genes, 2 categories)
  - +UBD_UBC(42 genes)
  - +UBD_UEV(1 genes)
    - Ag9G01358
- +ZnF(1 genes, 1 categories)
  - +ZnF_UBP(1 genes)
    - Ag9G01191
+ULD(100 genes, 2 categories)
- +UBL(4 genes, 2 categories)
  - +ATG8(3 genes)
  - +NEDD8(1 genes)
    - Ag5G02211
- +UDP(96 genes, 2 categories)
  - +UBQ(73 genes, 2 categories)
    - +UBQ_Other(54 genes)
    - +UBQ_PIM(19 genes)
  - +UFD(23 genes, 2 categories)
    - +PB1(12 genes)
    - +UBX(11 genes)