CAAX box proteins - Githubissues

ValWood commented 6 years ago

These are CAAX box proteins: Farnesyltransferase recognizes CaaX boxes where X = M, S, Q, A, or C, and a is aliphatic

SPAC24B11.10c cfh1 chitin synthase regulatory factor-like Cfh1 (predicted)
SPCC417.05c cfh2 chitin synthase regulatory factor Cfh2 (predicted)
SPBC1289.01c chr4 1,3-beta-glucan synthase regulatory factor Chf3/Chr4
SPAPB8E5.05 mfm1 M-factor precursor Mfm1
SPAC513.03 mfm2 M-factor precursor Mfm2
SPBPJ4664.03 mfm3 M-factor precursor Mfm3
SPAC17H9.09c ras1 GTPase Ras1
SPBC428.16c rhb1 Rheb GTPase Rhb1
SPAC16.01 rho2 Rho family GTPase Rho2
SPAC23C4.08 rho3 Rho family GTPase Rho3
SPBC530.04 mod5 Tea1 anchoring protein Mod5
SPAC12G12.11c miy1 Lys48-specific deubiquitinase Mindy family, Miy1
SPAC3C7.05c mug191 alpha-1,6- mannanase (predicted)
- SPBC13G1.11 ykt6 SNARE Ykt6 (predicted). (SGD: membrane localization due to prenylation at the carboxy-terminus)
- SPAC11H11.03c ATP-dependent polydeoxyribonucleotide 5'-hydroxyl-kinase activity implicated in DNA repair (predicted)
- SPAC6B12.07c ubiquitin-protein ligase E3 with SPX domain, human LORNRF1 ortholog

where did these come from, they don't have this motif? SPBC215.04 git11 heterotrimeric G protein gamma subunit Git11 SPAC16E8.08 pos1 Spa2 interacting protein Pos1 (GTPase interacting) SPAC23A1.04c mnl1 alpha mannosidase Mnl1 (predicted) SPBC12C2.09c izh2 Haemolysin-III family plasma membrane receptor implicated in zinc ion homeostasis Izh2 (predicted) SPAC30C2.07 Schizosaccharomyces specific protein SPAC806.04c protein L-glutamate O-methyltransferase, implicated in DDR SPAC17C9.14 pex19 Pex19 protein (predicted) SGD farnesylated residue SPBC14F5.10c ubiquitin-protein ligase E3, unknown biological role (predicted)

ValWood commented 6 years ago

1 weed out likely FP (wrong compartment etc) 2 annotate protein feature 3 annotate protein modification 4 Infer GO:0098753 anchored component of the cytoplasmic side of the plasma membrane

could do TAS and create a GO ref to describe?

ValWood commented 6 years ago

check also ypt3 ypt5 byr4 ryh1

ValWood commented 6 years ago

Geranylgeranyltransferase I recognizes CaaX boxes with X = L or E

nice ! SPAC13G6.12c chs1 chitin synthase I

SPAC1F7.04 rho1 Rho family GTPase Rho1 SPAC16A10.04 rho4 Rho family GTPase Rho4 SPAC20H4.11c rho5 Rho family GTPase Rho5 SPAC110.03 cdc42 Rho family GTPase Cdc42

SPAC30D11.11 izh3 ER membrane Haemolysin-III family protein involved in zinc homeostasis Izh3 (predicted)

SPAC26H5.08c bgl2 glucan beta-glucosidase Bgl2 (predicted) SPAC959.04c omh6 alpha-1,2-mannosyltransferase Omh6 (predicted)

SPBC1604.21c ptr3 ubiquitin activating enzyme E1 SPAC823.12 vps11 HOPs/CORVET complex biquitin protein ligase E3 subunit Vps11 SPACUNK4.20 dubious SPBC146.02 Schizosaccharomyces specific protein

Likely false positive: SPAC16.03c ura2 dihydroorotase Ura2

ValWood commented 4 years ago

https://github.com/The-Sequence-Ontology/SO-Ontologies/issues/479

ValWood commented 4 years ago

Also check lipid association for these

ValWood commented 4 years ago

id: SO:0002230 name: CAAX_box http://www.sequenceontology.org/browser/current_svn/term/SO:0002230

pombase / curation

CAAX box proteins #1684