Term issue: GTP and GDP bound forms of GTPases

[ValWood]

Hi,

I will be working on signalling pathways quite a bit this year and will be needing GTP and GDP bound forms of the characterised signalling GTPases.

Systematic ID Gene name Product description UniProt ID

SPAC1565.06c spg1 GTPase Spg1 P87027 (there is an entry for spg1 but it does not seem to represent a modified form?)

SPAC1F7.04 rho1 Rho family GTPase Rho1 Q09914 stimulating GS in its GTP-bound prenylated form (PMID:8887550 PMID:9491802).

SPBC337.13c gtr1 RagA GTPase Gtr1 O74824 SPCC777.05 gtr2 RagA GTPase Gtr2 O74544 https://pubmed.ncbi.nlm.nih.gov/22344254 https://pubmed.ncbi.nlm.nih.gov/29199950/

SPBC1703.10 ypt1 GTPase Ypt1 P11620 SPAC9E9.07c ypt2 GTPase Ypt2 P17609 SPAC1B3.11c ypt4 GTPase Ypt4 O13876 SPAC6F6.15 ypt5 GTPase Ypt5 P36586 SPBC405.04c ypt7 GTPase Ypt7 O94655 SPAPB1A10.10c ypt71 GTPase Ypt71 Q9HDY0 SPAC4C5.02c ryh1 Rab family GTPase Ryh1 P17608 SPAC18G6.03 ypt3 Rab11 family GTPase Ypt3 P17610 SPBC1289.03c spi1 Ran GTPase Spi1 P28748 SPBC428.16c rhb1 Rheb GTPase Rhb1 O94363 SPAC110.03 cdc42 Rho family GTPase Cdc42 Q01112 SPAC16.01 rho2 Rho family GTPase Rho2 Q10133 SPAC23C4.08 rho3 Rho family GTPase Rho3 O13928 SPAC16A10.04 rho4 Rho family GTPase Rho4 Q874R1 SPAC20H4.11c rho5 Rho family GTPase Rho5 Q9HE04 SPAC17H9.09c ras1 GTPase Ras1 P08647

The ones I have come across so far in the pathways I am modelling are in bold. The others are non-urgent since I don't require them at the moment, but it might be useful to add so I don't need to remember whether we have them or not. I will add some references to the above in a sec...

These 2 entities seem to represent the same thing? https://proconsortium.org/cgi-bin/textsearch_pro?query0=O74544&search.x=0&search.y=0&field0=ALLFLDS

[nataled]

I'll start working on them. The two entities you refer to are not the same, as one pertains to a particular strain of the other.

[ValWood]

Ah right. Everyone works largely on the same isogenic lab strain (972 h-). But all of our requests could be at the species level (to reduce complication), unless you want to duplicate everything as species/strain? I think we would only request a strain variation for a natural isolate, if we ever needed, where the protein sequence was different.

[nataled]

All PomBase requests are processed for the species level. What you are seeing at the strain level is a result of automated processing of UniProtKB/Swiss-Prot of the 'main' entries. However, whenever you make a request for a modified form, I also create a species-level version of that UniProtKB entry as an 'anchor', so to speak.

[ValWood]

Got it!

[nataled]

Hi Val, A good-sized chunk of these already exist in PRO, but I'll duplicate them here for completeness. The pre-existing ones are those whose ID don't start with PR:000059nnn. All the below terms are already visible on the web site and accessible via download of our between-releases file http://purl.obolibrary.org/obo/pr/pr-dev.obo

One question: You mentioned something concerning rho1 and its prenylated form. Are the GDP-bound and/or GTP-bound forms be created with mention of prenylation? If so, which, and--if known--which site? I can either revise the existing term(s) to account for the prenylation, or create additional prenylated+bound term(s).

Spom-cdc42/GDP+ PR:000050564
Spom-cdc42/GTP+ PR:000044799
Spom-gtr1/GDP+ PR:000050542
Spom-gtr1/GTP+ PR:000050543
Spom-gtr2/GDP+ PR:000050545
Spom-gtr2/GTP+ PR:000050546
Spom-ras1/GDP+ PR:000059646
Spom-ras1/GTP+ PR:000036979
Spom-rhb1/GDP+ PR:000059628
Spom-rhb1/GTP+ PR:000059629
Spom-rho1/GDP+ PR:000059592
Spom-rho1/GTP+ PR:000050473
Spom-rho2/GDP+ PR:000059634
Spom-rho2/GTP+ PR:000050251
Spom-rho3/GDP+ PR:000059637
Spom-rho3/GTP+ PR:000037031
Spom-rho4/GDP+ PR:000059640
Spom-rho4/GTP+ PR:000059641
Spom-rho5/GDP+ PR:000059643
Spom-rho5/GTP+ PR:000059644
Spom-ryh1/GDP+ PR:000059619
Spom-ryh1/GTP+ PR:000059620
Spom-spg1/GDP+ PR:000059589
Spom-spg1/GTP+ PR:000050507
Spom-spi1/GDP+ PR:000045536
Spom-spi1/GTP+ PR:000045538
Spom-ypt1/GDP+ PR:000059601
Spom-ypt1/GTP+ PR:000059602
Spom-ypt2/GDP+ PR:000059604
Spom-ypt2/GTP+ PR:000059605
Spom-ypt3/GDP+ PR:000059622
Spom-ypt3/GTP+ PR:000059623
Spom-ypt4/GDP+ PR:000059607
Spom-ypt4/GTP+ PR:000059608
Spom-ypt5/GDP+ PR:000059610
Spom-ypt5/GTP+ PR:000059611
Spom-ypt7/GDP+ PR:000059613
Spom-ypt7/GTP+ PR:000059614
Spom-ypt71/GDP+ PR:000059616
Spom-ypt71/GTP+ PR:000059617

[Term]
id: PR:000050564
name: cell division control protein 42, GDP-bound form (Schizosaccharomyces pombe)
def: "A cell division control protein 42 (Schizosaccharomyces pombe) that is non-covalently bound to GDP." [PRO:DAN, PomBase:VW, PMID:34382996]
comment: Category=organism-complex. Requested by=PomBase.
synonym: "Spom-cdc42/GDP+" EXACT PRO-short-label [PRO:DAN]
intersection_of: PR:000044798 ! cell division control protein 42 (Schizosaccharomyces pombe)
intersection_of: non-covalently_bound_to CHEBI:17552 ! GDP
relationship: only_in_taxon NCBITaxon:4896 ! Schizosaccharomyces pombe

[Term]
id: PR:000044799
name: cell division control protein 42, GTP-bound form (Schizosaccharomyces pombe)
def: "A cell division control protein 42 (Schizosaccharomyces pombe) that is non-covalently bound to GTP." [PRO:DAN, PomBase:MAH, PMID:26941334]
comment: Category=organism-complex. Requested by=PomBase.
synonym: "Spom-cdc42/GTP+" EXACT PRO-short-label [PRO:DAN]
intersection_of: PR:000044798 ! cell division control protein 42 (Schizosaccharomyces pombe)
intersection_of: non-covalently_bound_to CHEBI:15996 ! GTP
relationship: only_in_taxon NCBITaxon:4896 ! Schizosaccharomyces pombe

[Term]
id: PR:000050542
name: GTP-binding protein gtr1, GDP-bound form (Schizosaccharomyces pombe)
def: "A GTP-binding protein gtr1 (Schizosaccharomyces pombe) that is non-covalently bound to GDP." [PRO:DAN, PomBase:VW, PMID:27227887, PMID:33534698]
comment: Category=organism-complex. Requested by=PomBase.
synonym: "Spom-gtr1/GDP+" EXACT PRO-short-label [PRO:DAN]
intersection_of: PR:000050541 ! GTP-binding protein gtr1 (Schizosaccharomyces pombe)
intersection_of: non-covalently_bound_to CHEBI:17552 ! GDP
relationship: only_in_taxon NCBITaxon:4896 ! Schizosaccharomyces pombe

[Term]
id: PR:000050543
name: GTP-binding protein gtr1, GTP-bound form (Schizosaccharomyces pombe)
def: "A GTP-binding protein gtr1 (Schizosaccharomyces pombe) that is non-covalently bound to GTP." [PRO:DAN, PomBase:VW, PMID:27227887, PMID:33534698]
comment: Category=organism-complex. Requested by=PomBase.
synonym: "Spom-gtr1/GTP+" EXACT PRO-short-label [PRO:DAN]
intersection_of: PR:000050541 ! GTP-binding protein gtr1 (Schizosaccharomyces pombe)
intersection_of: non-covalently_bound_to CHEBI:15996 ! GTP
relationship: only_in_taxon NCBITaxon:4896 ! Schizosaccharomyces pombe

[Term]
id: PR:000050545
name: GTP-binding protein gtr2, GDP-bound form (Schizosaccharomyces pombe)
def: "A GTP-binding protein gtr2 (Schizosaccharomyces pombe) that is non-covalently bound to GDP." [PRO:DAN, PomBase:VW, PMID:27227887]
comment: Category=organism-complex. Requested by=PomBase.
synonym: "Spom-gtr2/GDP+" EXACT PRO-short-label [PRO:DAN]
intersection_of: PR:000050544 ! GTP-binding protein gtr2 (Schizosaccharomyces pombe)
intersection_of: non-covalently_bound_to CHEBI:17552 ! GDP
relationship: only_in_taxon NCBITaxon:4896 ! Schizosaccharomyces pombe

[Term]
id: PR:000050546
name: GTP-binding protein gtr2, GTP-bound form (Schizosaccharomyces pombe)
def: "A GTP-binding protein gtr2 (Schizosaccharomyces pombe) that is non-covalently bound to GTP." [PRO:DAN, PomBase:VW, PMID:27227887]
comment: Category=organism-complex. Requested by=PomBase.
synonym: "Spom-gtr2/GTP+" EXACT PRO-short-label [PRO:DAN]
intersection_of: PR:000050544 ! GTP-binding protein gtr2 (Schizosaccharomyces pombe)
intersection_of: non-covalently_bound_to CHEBI:15996 ! GTP
relationship: only_in_taxon NCBITaxon:4896 ! Schizosaccharomyces pombe

[Term]
id: PR:000059646
name: Ras-like protein 1, GDP-bound form (Schizosaccharomyces pombe)
def: "A Ras-like protein 1 (Schizosaccharomyces pombe) that is non-covalently bound to GDP." [PRO:DAN, PomBase:VW]
comment: Category=organism-complex. Requested by=PomBase.
synonym: "Spom-ras1/GDP+" EXACT PRO-short-label [PRO:DAN]
intersection_of: PR:000036978 ! Ras-like protein 1 (Schizosaccharomyces pombe)
intersection_of: non-covalently_bound_to CHEBI:17552 ! GDP
relationship: only_in_taxon NCBITaxon:4896 ! Schizosaccharomyces pombe

[Term]
id: PR:000036979
name: Ras-like protein 1, GTP-bound form (Schizosaccharomyces pombe)
def: "A Ras-like protein 1 (Schizosaccharomyces pombe) that is non-covalently bound to GTP." [PRO:DAN, PomBase:MAH, PMID:29453312]
comment: Category=organism-complex. Requested by=PomBase.
synonym: "Spom-ras1/GTP+" EXACT PRO-short-label [PRO:DAN]
intersection_of: PR:000036978 ! Ras-like protein 1 (Schizosaccharomyces pombe)
intersection_of: non-covalently_bound_to CHEBI:15996 ! GTP
relationship: only_in_taxon NCBITaxon:4896 ! Schizosaccharomyces pombe

[Term]
id: PR:000059628
name: GTP-binding protein rhb1, GDP-bound form (Schizosaccharomyces pombe)
def: "A GTP-binding protein rhb1 (Schizosaccharomyces pombe) that is non-covalently bound to GDP." [PRO:DAN, PomBase:VW]
comment: Category=organism-complex. Requested by=PomBase.
synonym: "Spom-rhb1/GDP+" EXACT PRO-short-label [PRO:DAN]
intersection_of: PR:000059627 ! GTP-binding protein rhb1 (Schizosaccharomyces pombe)
intersection_of: non-covalently_bound_to CHEBI:17552 ! GDP
relationship: only_in_taxon NCBITaxon:4896 ! Schizosaccharomyces pombe

[Term]
id: PR:000059629
name: GTP-binding protein rhb1, GTP-bound form (Schizosaccharomyces pombe)
def: "A GTP-binding protein rhb1 (Schizosaccharomyces pombe) that is non-covalently bound to GDP." [PRO:DAN, PomBase:VW]
comment: Category=organism-complex. Requested by=PomBase.
synonym: "Spom-rhb1/GTP+" EXACT PRO-short-label [PRO:DAN]
intersection_of: PR:000059627 ! GTP-binding protein rhb1 (Schizosaccharomyces pombe)
intersection_of: non-covalently_bound_to CHEBI:15996 ! GTP
relationship: only_in_taxon NCBITaxon:4896 ! Schizosaccharomyces pombe

[Term]
id: PR:000059592
name: GTP-binding protein rho1, GDP-bound form (Schizosaccharomyces pombe)
def: "A GTP-binding protein rho1 (Schizosaccharomyces pombe) that is non-covalently bound to GDP." [PRO:DAN, PomBase:VW]
comment: Category=organism-complex. Requested by=PomBase.
synonym: "Spom-rho1/GDP+" EXACT PRO-short-label [PRO:DAN]
intersection_of: PR:000050474 ! GTP-binding protein rho1 (Schizosaccharomyces pombe)
intersection_of: non-covalently_bound_to CHEBI:17552 ! GDP
relationship: only_in_taxon NCBITaxon:4896 ! Schizosaccharomyces pombe

[Term]
id: PR:000050473
name: GTP-binding protein rho1, GTP-bound form (Schizosaccharomyces pombe)
def: "A GTP-binding protein rho1 (Schizosaccharomyces pombe) that is non-covalently bound to GTP." [PRO:DAN, PomBase:VW, PMID:10651902]
comment: Category=organism-complex. Requested by=PomBase.
synonym: "Spom-rho1/GTP+" EXACT PRO-short-label [PRO:DAN]
intersection_of: PR:000050474 ! GTP-binding protein rho1 (Schizosaccharomyces pombe)
intersection_of: non-covalently_bound_to CHEBI:15996 ! GTP
relationship: only_in_taxon NCBITaxon:4896 ! Schizosaccharomyces pombe

[Term]
id: PR:000059634
name: GTP-binding protein rho2, GDP-bound form (Schizosaccharomyces pombe)
def: "A GTP-binding protein rho2 (Schizosaccharomyces pombe) that is non-covalently bound to GDP." [PRO:DAN, PomBase:VW]
comment: Category=organism-complex. Requested by=PomBase.
synonym: "Spom-rho2/GDP+" EXACT PRO-short-label [PRO:DAN]
intersection_of: PR:000050250 ! GTP-binding protein rho2 (Schizosaccharomyces pombe)
intersection_of: non-covalently_bound_to CHEBI:17552 ! GDP
relationship: only_in_taxon NCBITaxon:4896 ! Schizosaccharomyces pombe

[Term]
id: PR:000050251
name: GTP-binding protein rho2, GTP-bound form (Schizosaccharomyces pombe)
def: "A GTP-binding protein rho2 (Schizosaccharomyces pombe) that is non-covalently bound to GTP." [PRO:DAN, PomBase:MAH, PMID:26960792]
comment: Category=organism-complex. Requested by=PomBase.
synonym: "Spom-rho2/GTP+" EXACT PRO-short-label [PRO:DAN]
intersection_of: PR:000050250 ! GTP-binding protein rho2 (Schizosaccharomyces pombe)
intersection_of: non-covalently_bound_to CHEBI:15996 ! GTP
relationship: only_in_taxon NCBITaxon:4896 ! Schizosaccharomyces pombe

[Term]
id: PR:000059637
name: GTP-binding protein rho3, GDP-bound form (Schizosaccharomyces pombe)
def: "A GTP-binding protein rho3 (Schizosaccharomyces pombe) that is non-covalently bound to GDP." [PRO:DAN, PomBase:VW]
comment: Category=organism-complex. Requested by=PomBase.
synonym: "Spom-rho3/GDP+" EXACT PRO-short-label [PRO:DAN]
intersection_of: PR:000037030 ! GTP-binding protein rho3 (Schizosaccharomyces pombe)
intersection_of: non-covalently_bound_to CHEBI:17552 ! GDP
relationship: only_in_taxon NCBITaxon:4896 ! Schizosaccharomyces pombe

[Term]
id: PR:000037031
name: GTP-binding protein rho3, GTP-bound form (Schizosaccharomyces pombe)
def: "A GTP-binding protein rho3 (Schizosaccharomyces pombe) that is non-covalently bound to GTP." [PRO:DAN, PomBase:VW, PMID:24947517]
comment: Category=organism-complex. Requested by=PomBase.
synonym: "Spom-rho3/GTP+" EXACT PRO-short-label [PRO:DAN]
intersection_of: PR:000037030 ! GTP-binding protein rho3 (Schizosaccharomyces pombe)
intersection_of: non-covalently_bound_to CHEBI:15996 ! GTP
relationship: only_in_taxon NCBITaxon:4896 ! Schizosaccharomyces pombe

[Term]
id: PR:000059640
name: GTP-binding protein rho4, GDP-bound form (Schizosaccharomyces pombe)
def: "A GTP-binding protein rho4 (Schizosaccharomyces pombe) that is non-covalently bound to GDP." [PRO:DAN, PomBase:VW]
comment: Category=organism-complex. Requested by=PomBase.
synonym: "Spom-rho4/GDP+" EXACT PRO-short-label [PRO:DAN]
intersection_of: PR:000059639 ! GTP-binding protein rho4 (Schizosaccharomyces pombe)
intersection_of: non-covalently_bound_to CHEBI:17552 ! GDP
relationship: only_in_taxon NCBITaxon:4896 ! Schizosaccharomyces pombe

[Term]
id: PR:000059641
name: GTP-binding protein rho4, GTP-bound form (Schizosaccharomyces pombe)
def: "A GTP-binding protein rho4 (Schizosaccharomyces pombe) that is non-covalently bound to GDP." [PRO:DAN, PomBase:VW]
comment: Category=organism-complex. Requested by=PomBase.
synonym: "Spom-rho4/GTP+" EXACT PRO-short-label [PRO:DAN]
intersection_of: PR:000059639 ! GTP-binding protein rho4 (Schizosaccharomyces pombe)
intersection_of: non-covalently_bound_to CHEBI:15996 ! GTP
relationship: only_in_taxon NCBITaxon:4896 ! Schizosaccharomyces pombe

[Term]
id: PR:000059643
name: GTP-binding protein rho5, GDP-bound form (Schizosaccharomyces pombe)
def: "A GTP-binding protein rho5 (Schizosaccharomyces pombe) that is non-covalently bound to GDP." [PRO:DAN, PomBase:VW]
comment: Category=organism-complex. Requested by=PomBase.
synonym: "Spom-rho5/GDP+" EXACT PRO-short-label [PRO:DAN]
intersection_of: PR:000059642 ! GTP-binding protein rho5 (Schizosaccharomyces pombe)
intersection_of: non-covalently_bound_to CHEBI:17552 ! GDP
relationship: only_in_taxon NCBITaxon:4896 ! Schizosaccharomyces pombe

[Term]
id: PR:000059644
name: GTP-binding protein rho5, GTP-bound form (Schizosaccharomyces pombe)
def: "A GTP-binding protein rho5 (Schizosaccharomyces pombe) that is non-covalently bound to GDP." [PRO:DAN, PomBase:VW]
comment: Category=organism-complex. Requested by=PomBase.
synonym: "Spom-rho5/GTP+" EXACT PRO-short-label [PRO:DAN]
intersection_of: PR:000059642 ! GTP-binding protein rho5 (Schizosaccharomyces pombe)
intersection_of: non-covalently_bound_to CHEBI:15996 ! GTP
relationship: only_in_taxon NCBITaxon:4896 ! Schizosaccharomyces pombe

[Term]
id: PR:000059619
name: GTP-binding protein ryh1, GDP-bound form (Schizosaccharomyces pombe)
def: "A GTP-binding protein ryh1 (Schizosaccharomyces pombe) that is non-covalently bound to GDP." [PRO:DAN, PomBase:VW]
comment: Category=organism-complex. Requested by=PomBase.
synonym: "Spom-ryh1/GDP+" EXACT PRO-short-label [PRO:DAN]
intersection_of: PR:000059618 ! GTP-binding protein ryh1 (Schizosaccharomyces pombe)
intersection_of: non-covalently_bound_to CHEBI:17552 ! GDP
relationship: only_in_taxon NCBITaxon:4896 ! Schizosaccharomyces pombe

[Term]
id: PR:000059620
name: GTP-binding protein ryh1, GTP-bound form (Schizosaccharomyces pombe)
def: "A GTP-binding protein ryh1 (Schizosaccharomyces pombe) that is non-covalently bound to GDP." [PRO:DAN, PomBase:VW]
comment: Category=organism-complex. Requested by=PomBase.
synonym: "Spom-ryh1/GTP+" EXACT PRO-short-label [PRO:DAN]
intersection_of: PR:000059618 ! GTP-binding protein ryh1 (Schizosaccharomyces pombe)
intersection_of: non-covalently_bound_to CHEBI:15996 ! GTP
relationship: only_in_taxon NCBITaxon:4896 ! Schizosaccharomyces pombe

[Term]
id: PR:000059589
name: septum-promoting GTP-binding protein 1, GDP-bound form (Schizosaccharomyces pombe)
def: "A septum-promoting GTP-binding protein 1 (Schizosaccharomyces pombe) that is non-covalently bound to GDP." [PRO:DAN, PomBase:VW]
comment: Category=organism-complex. Requested by=PomBase.
synonym: "Spom-spg1/GDP+" EXACT PRO-short-label [PRO:DAN]
intersection_of: PR:000050506 ! septum-promoting GTP-binding protein 1 (Schizosaccharomyces pombe)
intersection_of: non-covalently_bound_to CHEBI:17552 ! GDP
relationship: only_in_taxon NCBITaxon:4896 ! Schizosaccharomyces pombe

[Term]
id: PR:000050507
name: septum-promoting GTP-binding protein 1, GTP-bound form (Schizosaccharomyces pombe)
def: "A septum-promoting GTP-binding protein 1 (Schizosaccharomyces pombe) that is non-covalently bound to GTP." [PRO:DAN, PomBase:VW, PMID:9420333]
comment: Category=organism-complex. Requested by=PomBase.
synonym: "Spom-spg1/GTP+" EXACT PRO-short-label [PRO:DAN]
intersection_of: PR:000050506 ! septum-promoting GTP-binding protein 1 (Schizosaccharomyces pombe)
intersection_of: non-covalently_bound_to CHEBI:15996 ! GTP
relationship: only_in_taxon NCBITaxon:4896 ! Schizosaccharomyces pombe

[Term]
id: PR:000045536
name: GTP-binding nuclear protein spi1, GDP-bound form (Schizosaccharomyces pombe)
def: "A GTP-binding nuclear protein spi1 (Schizosaccharomyces pombe) that is non-covalently bound to GDP." [PRO:CNA, PRO:DAN, PomBase:MAH, PMID:18422602]
comment: Category=organism-complex. Requested by=PomBase.
synonym: "Spom-spi1/GDP+" EXACT PRO-short-label [PRO:DAN]
synonym: "Spi1-GDP (Schizosaccharomyces pombe)" EXACT []
synonym: "Ran-GDP" BROAD [PRO:DNx]
intersection_of: PR:000045537 ! GTP-binding nuclear protein spi1 (Schizosaccharomyces pombe)
intersection_of: non-covalently_bound_to CHEBI:17552 ! GDP
relationship: only_in_taxon NCBITaxon:4896 ! Schizosaccharomyces pombe

[Term]
id: PR:000045538
name: GTP-binding nuclear protein spi1, GTP-bound form (Schizosaccharomyces pombe)
def: "A GTP-binding nuclear protein spi1 (Schizosaccharomyces pombe) that is non-covalently bound to GTP." [PRO:CNA, PMID:18422602]
comment: Category=organism-complex. Requested by=PomBase.
synonym: "Spom-spi1/GTP+" EXACT PRO-short-label [PRO:DAN]
synonym: "Ran-GTP" BROAD [PRO:DNx]
intersection_of: PR:000045537 ! GTP-binding nuclear protein spi1 (Schizosaccharomyces pombe)
intersection_of: non-covalently_bound_to CHEBI:15996 ! GTP
relationship: only_in_taxon NCBITaxon:4896 ! Schizosaccharomyces pombe

[Term]
id: PR:000059601
name: GTP-binding protein ypt1, GDP-bound form (Schizosaccharomyces pombe)
def: "A GTP-binding protein ypt1 (Schizosaccharomyces pombe) that is non-covalently bound to GDP." [PRO:DAN, PomBase:VW]
comment: Category=organism-complex. Requested by=PomBase.
synonym: "Spom-ypt1/GDP+" EXACT PRO-short-label [PRO:DAN]
intersection_of: PR:000059600 ! GTP-binding protein ypt1 (Schizosaccharomyces pombe)
intersection_of: non-covalently_bound_to CHEBI:17552 ! GDP
relationship: only_in_taxon NCBITaxon:4896 ! Schizosaccharomyces pombe

[Term]
id: PR:000059602
name: GTP-binding protein ypt1, GTP-bound form (Schizosaccharomyces pombe)
def: "A GTP-binding protein ypt1 (Schizosaccharomyces pombe) that is non-covalently bound to GDP." [PRO:DAN, PomBase:VW]
comment: Category=organism-complex. Requested by=PomBase.
synonym: "Spom-ypt1/GTP+" EXACT PRO-short-label [PRO:DAN]
intersection_of: PR:000059600 ! GTP-binding protein ypt1 (Schizosaccharomyces pombe)
intersection_of: non-covalently_bound_to CHEBI:15996 ! GTP
relationship: only_in_taxon NCBITaxon:4896 ! Schizosaccharomyces pombe

[Term]
id: PR:000059604
name: GTP-binding protein ypt2, GDP-bound form (Schizosaccharomyces pombe)
def: "A GTP-binding protein ypt2 (Schizosaccharomyces pombe) that is non-covalently bound to GDP." [PRO:DAN, PomBase:VW]
comment: Category=organism-complex. Requested by=PomBase.
synonym: "Spom-ypt2/GDP+" EXACT PRO-short-label [PRO:DAN]
intersection_of: PR:000059603 ! GTP-binding protein ypt2 (Schizosaccharomyces pombe)
intersection_of: non-covalently_bound_to CHEBI:17552 ! GDP
relationship: only_in_taxon NCBITaxon:4896 ! Schizosaccharomyces pombe

[Term]
id: PR:000059605
name: GTP-binding protein ypt2, GTP-bound form (Schizosaccharomyces pombe)
def: "A GTP-binding protein ypt2 (Schizosaccharomyces pombe) that is non-covalently bound to GDP." [PRO:DAN, PomBase:VW]
comment: Category=organism-complex. Requested by=PomBase.
synonym: "Spom-ypt2/GTP+" EXACT PRO-short-label [PRO:DAN]
intersection_of: PR:000059603 ! GTP-binding protein ypt2 (Schizosaccharomyces pombe)
intersection_of: non-covalently_bound_to CHEBI:15996 ! GTP
relationship: only_in_taxon NCBITaxon:4896 ! Schizosaccharomyces pombe

[Term]
id: PR:000059622
name: GTP-binding protein ypt3, GDP-bound form (Schizosaccharomyces pombe)
def: "A GTP-binding protein ypt3 (Schizosaccharomyces pombe) that is non-covalently bound to GDP." [PRO:DAN, PomBase:VW]
comment: Category=organism-complex. Requested by=PomBase.
synonym: "Spom-ypt3/GDP+" EXACT PRO-short-label [PRO:DAN]
intersection_of: PR:000059621 ! GTP-binding protein ypt3 (Schizosaccharomyces pombe)
intersection_of: non-covalently_bound_to CHEBI:17552 ! GDP
relationship: only_in_taxon NCBITaxon:4896 ! Schizosaccharomyces pombe

[Term]
id: PR:000059623
name: GTP-binding protein ypt3, GTP-bound form (Schizosaccharomyces pombe)
def: "A GTP-binding protein ypt3 (Schizosaccharomyces pombe) that is non-covalently bound to GDP." [PRO:DAN, PomBase:VW]
comment: Category=organism-complex. Requested by=PomBase.
synonym: "Spom-ypt3/GTP+" EXACT PRO-short-label [PRO:DAN]
intersection_of: PR:000059621 ! GTP-binding protein ypt3 (Schizosaccharomyces pombe)
intersection_of: non-covalently_bound_to CHEBI:15996 ! GTP
relationship: only_in_taxon NCBITaxon:4896 ! Schizosaccharomyces pombe

[Term]
id: PR:000059607
name: GTP-binding protein ypt4, GDP-bound form (Schizosaccharomyces pombe)
def: "A GTP-binding protein ypt4 (Schizosaccharomyces pombe) that is non-covalently bound to GDP." [PRO:DAN, PomBase:VW]
comment: Category=organism-complex. Requested by=PomBase.
synonym: "Spom-ypt4/GDP+" EXACT PRO-short-label [PRO:DAN]
intersection_of: PR:000059606 ! GTP-binding protein ypt4 (Schizosaccharomyces pombe)
intersection_of: non-covalently_bound_to CHEBI:17552 ! GDP
relationship: only_in_taxon NCBITaxon:4896 ! Schizosaccharomyces pombe

[Term]
id: PR:000059608
name: GTP-binding protein ypt4, GTP-bound form (Schizosaccharomyces pombe)
def: "A GTP-binding protein ypt4 (Schizosaccharomyces pombe) that is non-covalently bound to GDP." [PRO:DAN, PomBase:VW]
comment: Category=organism-complex. Requested by=PomBase.
synonym: "Spom-ypt4/GTP+" EXACT PRO-short-label [PRO:DAN]
intersection_of: PR:000059606 ! GTP-binding protein ypt4 (Schizosaccharomyces pombe)
intersection_of: non-covalently_bound_to CHEBI:15996 ! GTP
relationship: only_in_taxon NCBITaxon:4896 ! Schizosaccharomyces pombe

[Term]
id: PR:000059610
name: GTP-binding protein ypt5, GDP-bound form (Schizosaccharomyces pombe)
def: "A GTP-binding protein ypt5 (Schizosaccharomyces pombe) that is non-covalently bound to GDP." [PRO:DAN, PomBase:VW]
comment: Category=organism-complex. Requested by=PomBase.
synonym: "Spom-ypt5/GDP+" EXACT PRO-short-label [PRO:DAN]
intersection_of: PR:000030005 ! GTP-binding protein ypt5 (Schizosaccharomyces pombe)
intersection_of: non-covalently_bound_to CHEBI:17552 ! GDP
relationship: only_in_taxon NCBITaxon:4896 ! Schizosaccharomyces pombe

[Term]
id: PR:000059611
name: GTP-binding protein ypt5, GTP-bound form (Schizosaccharomyces pombe)
def: "A GTP-binding protein ypt5 (Schizosaccharomyces pombe) that is non-covalently bound to GDP." [PRO:DAN, PomBase:VW]
comment: Category=organism-complex. Requested by=PomBase.
synonym: "Spom-ypt5/GTP+" EXACT PRO-short-label [PRO:DAN]
intersection_of: PR:000030005 ! GTP-binding protein ypt5 (Schizosaccharomyces pombe)
intersection_of: non-covalently_bound_to CHEBI:15996 ! GTP
relationship: only_in_taxon NCBITaxon:4896 ! Schizosaccharomyces pombe

[Term]
id: PR:000059613
name: Ypt/Rab-type GTPase ypt7, GDP-bound form (Schizosaccharomyces pombe)
def: "A Ypt/Rab-type GTPase ypt7 (Schizosaccharomyces pombe) that is non-covalently bound to GDP." [PRO:DAN, PomBase:VW]
comment: Category=organism-complex. Requested by=PomBase.
synonym: "Spom-ypt7/GDP+" EXACT PRO-short-label [PRO:DAN]
intersection_of: PR:000059612 ! Ypt/Rab-type GTPase ypt7 (Schizosaccharomyces pombe)
intersection_of: non-covalently_bound_to CHEBI:17552 ! GDP
relationship: only_in_taxon NCBITaxon:4896 ! Schizosaccharomyces pombe

[Term]
id: PR:000059614
name: Ypt/Rab-type GTPase ypt7, GTP-bound form (Schizosaccharomyces pombe)
def: "A Ypt/Rab-type GTPase ypt7 (Schizosaccharomyces pombe) that is non-covalently bound to GDP." [PRO:DAN, PomBase:VW]
comment: Category=organism-complex. Requested by=PomBase.
synonym: "Spom-ypt7/GTP+" EXACT PRO-short-label [PRO:DAN]
intersection_of: PR:000059612 ! Ypt/Rab-type GTPase ypt7 (Schizosaccharomyces pombe)
intersection_of: non-covalently_bound_to CHEBI:15996 ! GTP
relationship: only_in_taxon NCBITaxon:4896 ! Schizosaccharomyces pombe

[Term]
id: PR:000059616
name: Ypt/Rab-type GTPase ypt71, GDP-bound form (Schizosaccharomyces pombe)
def: "A Ypt/Rab-type GTPase ypt71 (Schizosaccharomyces pombe) that is non-covalently bound to GDP." [PRO:DAN, PomBase:VW]
comment: Category=organism-complex. Requested by=PomBase.
synonym: "Spom-ypt71/GDP+" EXACT PRO-short-label [PRO:DAN]
intersection_of: PR:000059615 ! Ypt/Rab-type GTPase ypt71 (Schizosaccharomyces pombe)
intersection_of: non-covalently_bound_to CHEBI:17552 ! GDP
relationship: only_in_taxon NCBITaxon:4896 ! Schizosaccharomyces pombe

[Term]
id: PR:000059617
name: Ypt/Rab-type GTPase ypt71, GTP-bound form (Schizosaccharomyces pombe)
def: "A Ypt/Rab-type GTPase ypt71 (Schizosaccharomyces pombe) that is non-covalently bound to GDP." [PRO:DAN, PomBase:VW]
comment: Category=organism-complex. Requested by=PomBase.
synonym: "Spom-ypt71/GTP+" EXACT PRO-short-label [PRO:DAN]
intersection_of: PR:000059615 ! Ypt/Rab-type GTPase ypt71 (Schizosaccharomyces pombe)
intersection_of: non-covalently_bound_to CHEBI:15996 ! GTP
relationship: only_in_taxon NCBITaxon:4896 ! Schizosaccharomyces pombe

[ValWood]

Hi @nataled sorry for the delay.

. I can find evidence for prenylation for Rho1-5 , ras1, rhb1 and cdc42. So I guess the GDP/GTP bound forms of these should also be prenylated? This will always be true (so I would not use the non-prenylated from in annotation).

It is possible some of the membrane localized GTPases are only palmitoylated (reversible) as opposed to prenylated (irreversible), but I don't know this right now. I will ask the authors about this next time I am annotating GTPases.

[nataled]

Okay, I will revise those entries to be both prenylated and bound.

[nataled]

@ValWood I forgot to ask: are the GDP/GTP bound forms always prenylated? That is, every GDP/GTP bound form is created from already-prenylated proteins?

[ValWood]

I think the functional GTP/GDP bound forms are always prenylated. My feeling is that If they are not prenylated they would not be correctly localised but I will need to check this with experts. I would like to use this as a training example for our new starter (which won't be for a couple of months) so there is no hurry fo me. Can we have the ticket pending for a while, I still have it on my radar.

[nataled]

Sure, that's fine. I have a tag specifically for that :)