Sorry for the delay, I was away. I created a number of terms based on your request. The specific terms you requested are PR:000044611 for the phosphorylated sid4, and PR:000044743 for the unmodified dma1. A few notes on the above:
1) The paper you cite doesn't describe the phosphorylated sid4, only mentions it. I found the description in another paper.
2) Because of the above, I wondered if you actually wanted the ubiquitinated sid4. So I made it just in case. A full accounting of the entire process will need this term anyway.
3) The version of 'unmodified dma1' that I made is actually 'non-ubiquitinated dma1'. The paper indicates that dma1 is phosphorylated, so it technically isn't truly unmodified. I suspect you needed unmodified with respect to ubiquitination.
4) For the purpose of full accounting of the process, and because it is a major topic for the paper, I also made a ubiquitinated form of dma1.
Please let me know if you detect any problems.
Best regards,
Darren
[Term]
id: PR:000044588
name: septation initiation protein sid4 (Schizosaccharomyces pombe)
def: "A protein that is a translation product of the sid4 gene in Schizosaccharomyces pombe." [PRO:DAN]
comment: Category=organism-gene. Requested by=PomBase.
synonym: "Spom-sid4" EXACT PRO-short-label [PRO:DAN]
intersection_of: PR:000000001 ! protein
intersection_of: only_in_taxon NCBITaxon:4896 ! Schizosaccharomyces pombe
intersection_of: has_gene_template PomBase:SPBC244.01c ! sid4 (Schizosaccharomyces pombe)
[Term]
id: PR:000044611
name: septation initiation protein sid4 phosphorylated 1 (Schizosaccharomyces pombe)
def: "A septation initiation protein sid4 (Schizosaccharomyces pombe) that has been phosphorylated at the positions equivalent to Thr-275 and Ser-278 of the amino acid sequence represented by UniProtKB:O60187. Example: UniProtKB:O60187, Thr-275, MOD:00047|Ser-278, MOD:00046." [PRO:DAN, PomBase:VW, PMID:24055157]
comment: Category=organism-modification. Requested by=PomBase. Kinase=("hhp1/hhp2"; PR:000044624; Thr-275/Thr-278). Evidence=(ECO:0000006, based on PMID:24055157). Note: Phosphorylation at the indicated positions is necessary and sufficient for subsequent ubiquitination by dma1.
synonym: "Spom-sid4/Phos:1" EXACT PRO-short-label [PRO:DAN]
is_a: PR:000044588 ! septation initiation protein sid4 (Schizosaccharomyces pombe)
relationship: only_in_taxon NCBITaxon:4896 ! Schizosaccharomyces pombe
relationship: has_part MOD:00046 ! O-phospho-L-serine
relationship: has_part MOD:00047 ! O-phospho-L-threonine
[Term]
id: PR:000044612
name: septation initiation protein sid4 phosphorylated 1 ubiquitinated form (Schizosaccharomyces pombe)
def: "A septation initiation protein sid4 phosphorylated 1 (Schizosaccharomyces pombe) that includes at least one ubiquitinated lysine. Example: UniProtKB:O60187, Thr-275, MOD:00047|Ser-278, MOD:00046|MOD:01148." [PRO:DAN, PomBase:VW, PMID:24055157, PMID:21131906]
comment: Category=organism-modification. Requested by=PomBase. UbLigase=("dma1", PR:000044741). Evidence=(ECO:0000006, based on PMID:21131906).
synonym: "Spom-sid4/PhosUbiqLys+" EXACT PRO-short-label [PRO:DAN]
is_a: PR:000044611 ! septation initiation protein sid4 phosphorylated 1 (Schizosaccharomyces pombe)
relationship: has_part MOD:00046 ! O-phospho-L-serine
relationship: has_part MOD:00047 ! O-phospho-L-threonine
relationship: has_part MOD:01148 ! ubiquitinylated lysine
[Term]
id: PR:000044624
name: CK1 homologs hhp1/hhp2 (Schizosaccharomyces pombe)
def: "A protein that is a translation product of either the hhp1 or the hhp2 gene in Schizosaccharomyces pombe." [PRO:DAN]
comment: Category=organism-family. Requested by=PomBase. Note: These serine/threonine kinases are responsible for phosphorylation of sid4 as part of the septation initiation network (SIN). Three additional CK1 homologs (cki1, cki2, cki3) were not found to be needed for this process. [PMID:24055157]
synonym: "Spom-hhp[1/2]" EXACT PRO-short-label [PRO:DAN]
is_a: PR:000000001 ! protein
[Term]
id: PR:000044742
name: E3 ubiquitin-protein ligase dma1 ubiquitinated form (Schizosaccharomyces pombe)
def: "An E3 ubiquitin-protein ligase dma1 (Schizosaccharomyces pombe) that has been auto-ubiquitinated." [PRO:DAN, PomBase:VW, PMID:29975113]
comment: Category=organism-modification. Requested by=PomBase. Note: The precise combinations of ubiquitinated sites on any given molecule are not known. However, in vivo the following were found to be ubiquitinated at some point during the cell cycle: Lys-3, Lys-26, Lys-54, Lys-82, Lys-124, Lys-164, Lys-174, Lys-237, Lys-262.
Thanks, you are never slow, believe me. I only created the ticket 2 days ago! This is the fastest tracker!
I wanted to capture that dma1 (unubiquitinated) only binds to phosphorylated sid4
to negatively regulated SIN signalling. So the other ref was the correct one for phosphorylated sid4.
Thanks for figuring that out.
Val
If you would like to refer to this comment somewhere else in this project, copy and paste the following link:
Hi Val,
Sorry for the delay, I was away. I created a number of terms based on your request. The specific terms you requested are PR:000044611 for the phosphorylated sid4, and PR:000044743 for the unmodified dma1. A few notes on the above:
1) The paper you cite doesn't describe the phosphorylated sid4, only mentions it. I found the description in another paper.
2) Because of the above, I wondered if you actually wanted the ubiquitinated sid4. So I made it just in case. A full accounting of the entire process will need this term anyway.
3) The version of 'unmodified dma1' that I made is actually 'non-ubiquitinated dma1'. The paper indicates that dma1 is phosphorylated, so it technically isn't truly unmodified. I suspect you needed unmodified with respect to ubiquitination.
4) For the purpose of full accounting of the process, and because it is a major topic for the paper, I also made a ubiquitinated form of dma1.
Please let me know if you detect any problems.
Best regards,
Darren
[Term]
id: PR:000044588
name: septation initiation protein sid4 (Schizosaccharomyces pombe)
def: "A protein that is a translation product of the sid4 gene in Schizosaccharomyces pombe." [PRO:DAN]
comment: Category=organism-gene. Requested by=PomBase.
synonym: "Spom-sid4" EXACT PRO-short-label [PRO:DAN]
intersection_of: PR:000000001 ! protein
intersection_of: only_in_taxon NCBITaxon:4896 ! Schizosaccharomyces pombe
intersection_of: has_gene_template PomBase:SPBC244.01c ! sid4 (Schizosaccharomyces pombe)
[Term]
id: PR:000044611
name: septation initiation protein sid4 phosphorylated 1 (Schizosaccharomyces pombe)
def: "A septation initiation protein sid4 (Schizosaccharomyces pombe) that has been phosphorylated at the positions equivalent to Thr-275 and Ser-278 of the amino acid sequence represented by UniProtKB:O60187. Example: UniProtKB:O60187, Thr-275, MOD:00047|Ser-278, MOD:00046." [PRO:DAN, PomBase:VW, PMID:24055157]
comment: Category=organism-modification. Requested by=PomBase. Kinase=("hhp1/hhp2"; PR:000044624; Thr-275/Thr-278). Evidence=(ECO:0000006, based on PMID:24055157). Note: Phosphorylation at the indicated positions is necessary and sufficient for subsequent ubiquitination by dma1.
synonym: "Spom-sid4/Phos:1" EXACT PRO-short-label [PRO:DAN]
is_a: PR:000044588 ! septation initiation protein sid4 (Schizosaccharomyces pombe)
relationship: only_in_taxon NCBITaxon:4896 ! Schizosaccharomyces pombe
relationship: has_part MOD:00046 ! O-phospho-L-serine
relationship: has_part MOD:00047 ! O-phospho-L-threonine
[Term]
id: PR:000044612
name: septation initiation protein sid4 phosphorylated 1 ubiquitinated form (Schizosaccharomyces pombe)
def: "A septation initiation protein sid4 phosphorylated 1 (Schizosaccharomyces pombe) that includes at least one ubiquitinated lysine. Example: UniProtKB:O60187, Thr-275, MOD:00047|Ser-278, MOD:00046|MOD:01148." [PRO:DAN, PomBase:VW, PMID:24055157, PMID:21131906]
comment: Category=organism-modification. Requested by=PomBase. UbLigase=("dma1", PR:000044741). Evidence=(ECO:0000006, based on PMID:21131906).
synonym: "Spom-sid4/PhosUbiqLys+" EXACT PRO-short-label [PRO:DAN]
is_a: PR:000044611 ! septation initiation protein sid4 phosphorylated 1 (Schizosaccharomyces pombe)
relationship: has_part MOD:00046 ! O-phospho-L-serine
relationship: has_part MOD:00047 ! O-phospho-L-threonine
relationship: has_part MOD:01148 ! ubiquitinylated lysine
[Term]
id: PR:000044624
name: CK1 homologs hhp1/hhp2 (Schizosaccharomyces pombe)
def: "A protein that is a translation product of either the hhp1 or the hhp2 gene in Schizosaccharomyces pombe." [PRO:DAN]
comment: Category=organism-family. Requested by=PomBase. Note: These serine/threonine kinases are responsible for phosphorylation of sid4 as part of the septation initiation network (SIN). Three additional CK1 homologs (cki1, cki2, cki3) were not found to be needed for this process. [PMID:24055157]
synonym: "Spom-hhp[1/2]" EXACT PRO-short-label [PRO:DAN]
is_a: PR:000000001 ! protein
[Term]
id: PR:000044741
name: E3 ubiquitin-protein ligase dma1 (Schizosaccharomyces pombe)
def: "An E3 ubiquitin-protein ligase dma1 that is encoded in the genome of Schizosaccharomyces pombe." [PRO:DAN]
comment: Category=organism-gene. Requested by=PomBase.
synonym: "Spom-dma1" EXACT PRO-short-label [PRO:DAN]
intersection_of: PR:000027845 ! E3 ubiquitin-protein ligase dma1
intersection_of: only_in_taxon NCBITaxon:4896 ! Schizosaccharomyces pombe
relationship: has_gene_template PomBase:SPAC17G8.10c ! dma1 (Schizosaccharomyces pombe)
relationship: has_canonical_sequence UniProtKB:Q10322 ! Q10322-1
[Term]
id: PR:000044742
name: E3 ubiquitin-protein ligase dma1 ubiquitinated form (Schizosaccharomyces pombe)
def: "An E3 ubiquitin-protein ligase dma1 (Schizosaccharomyces pombe) that has been auto-ubiquitinated." [PRO:DAN, PomBase:VW, PMID:29975113]
comment: Category=organism-modification. Requested by=PomBase. Note: The precise combinations of ubiquitinated sites on any given molecule are not known. However, in vivo the following were found to be ubiquitinated at some point during the cell cycle: Lys-3, Lys-26, Lys-54, Lys-82, Lys-124, Lys-164, Lys-174, Lys-237, Lys-262.
synonym: "Spom-dma1/UbiqLys+" EXACT PRO-short-label [PRO:DAN]
intersection_of: PR:000044741 ! E3 ubiquitin-protein ligase dma1 (Schizosaccharomyces pombe)
intersection_of: only_in_taxon NCBITaxon:4896 ! Schizosaccharomyces pombe
relationship: has_part MOD:01148 ! ubiquitinylated lysine
[Term]
id: PR:000044743
name: E3 ubiquitin-protein ligase dma1 non-ubiquitinated form (Schizosaccharomyces pombe)
def: "An E3 ubiquitin-protein ligase dma1 (Schizosaccharomyces pombe) that lacks ubiquitinated lysine." [PRO:DAN, PomBase:VW, PMID:29975113]
comment: Category=organism-modification. Requested by=PomBase.
synonym: "Spom-dma1/UnUbiq" EXACT PRO-short-label [PRO:DAN]
intersection_of: PR:000044741 ! E3 ubiquitin-protein ligase dma1 (Schizosaccharomyces pombe)
intersection_of: only_in_taxon NCBITaxon:4896 ! Schizosaccharomyces pombe
relationship: lacks_part MOD:01148 ! ubiquitinylated lysine
Thanks, you are never slow, believe me. I only created the ticket 2 days ago! This is the fastest tracker!
I wanted to capture that dma1 (unubiquitinated) only binds to phosphorylated sid4
to negatively regulated SIN signalling. So the other ref was the correct one for phosphorylated sid4.
Thanks for figuring that out.
Val