proteins classed as "inferred process" but no slim process annotation

[ValWood]

• [x] SPBC1861.02 abp2 call this uncharacterised -> colour 10, no follow up in 20 years
• [x] SPAC3A11.02 cps3, revert to unknown, no characterisation
• [x] SPBC14C8.09c dbl3, changed to 10, no indfo other than ds-break binding
• [x] SPBC17D11.08 regulation of DNA replication P61962
• [x] SPBC646.17c microtubule cytoskeleton process IC GO:0005868
• [x] SPBC146.04 protein refolding? P55789
• [x] SPBC354.01 colour7
• [x] SPBC2G2.04c ADD isoleucine biosynthetic process S000001313
• [x] SPAC343.07 UNKNOWN
• [x] SPAC630.09c UNKNOWN
• [x] SPBC713.11c
• [x] SPAC19D5.04 GO:0006364 SGD
• [x] SPCC1442.16c detoxification Q08257
• [x] SPAC3A12.08 acyl-CoA metabolic process Q5T1C6
• [x] SPAC4H3.01
• [x] SPAC823.09c
• [x] SPAPB2B4.06 fatty acid metabolic process Q5T1C6
• [x] SPBC17A3.05c chaperone cofactor-dependent protein refolding
• [x] SPBC4.06 ADD phospholipid metabolic process Q9NPH0
• [x] SPBC2D10.20
• [x] SPBC211.07c
• [x] SPAC1071.09c UNKNOWN
• [x] SPBC56F2.03 ADD microtubule based transport IC from dynactin
• [x] SPCC61.03 -> ISS NAD biosynthesis via nicotinamide riboside salvage pathway
• [x] SPAC24C9.14 otu1 IS This published?
• [x] SPAC1952.03 otu2 IS This published?
• [x] SPAC3F10.15c spo12, quite a few papers but no process (called unknown as there doesn't seem to be anything clear)
• [x] SPBC649.04 uvi15
• [x] SPCC16C4.07 RNA-binding protein Scw1, published (curated paper)
• [x] SPBC20F10.10 cyclin psl1 had to go with NAS to "regulation of cell cycle transition" which seems safe as cerevisiae orthologs are cdk1 binding partners. Reverted from published to inferred as I can't find any functional info
• [x] SPBC18H10.15 cdk11 https://github.com/pombase/curation/issues/1565 added an NAS which will be filtered when the curation comes through

published in some depth but no biological role, ignore for now

• [ ] SPBC839.07 ask Susan
• [ ] SPAC1071.12c stp1 quite a few papers but no process published, unkown role

published recently but not curated

• [ ] SPCC4G3.11 published but not curated nur1 PMID:27451393

• [ ] SPBC29A10.12 PUBLISHED 2017

• [ ] ptf1 PMID:22184112

• [ ] SPAC12B10.14c tea5 where is name from as I can't find any papers, ask @haylesjv

• [ ] SPBP35G2.02 26S proteasome co-factor Txc1

• [ ] SPAC4F10.04 protein phosphatase type 2A regulator, PTPA family Ypa1

• [ ] SPAC1782.05 protein phosphatase type 2A regulator, PTPA family Ypa2

mtr

• [ ] SPBC1711.02 m-t-r
• [ ] SPMTR.04 m-t-r
• [ ] SPMTR.03 m-t-r

signalling

• [x] SPAC2F7.02c sounds like signalling, but no term
• [x] SPBC1271.03c sounds like signalling, but no term.
• [x] SPBC216.01c -> signalling

other

• [ ] SPBC1289.16c copper amine oxidase, what process? possibly non-functional
• [x] SPBC8D2.01 protein degradation???
• [x] SPAC1039.11c alpha-glucosidase
• [x] SPAC25H1.09 ADD fungal-type cell wall biogenesis
• [ ] SPCC16C4.12 ADD protein maturation
• [ ] SPBC21B10.05c @Antonialock torc process?
• [x] SPAC823.14 L-serine biosynthetic process P78330???? not sure transferred to https://github.com/pombase/curation/issues/1633
• [x] SPBC1734.05c mRNA splicing, via spliceosome but TAS reactome, trace paper mail UniProt - https://github.com/pombase/curation/issues/1632
• [x] SPAC1039.06 alanine racemase - > D-serine ammonia-lyase activity
• [x] SPAC186.06 FIXED…actually where does the process come from, we did not curate this paper
• [x] SPAC27E2.01 alpha-amylase
• [ ] SPAC9.02c sgd has chromatin organization , seems odd
• [x] SPAPB24D3.03 agmatinase
• [x] SPBC16E9.15 http://www.uniprot.org/uniprot/O75506 check for EXP for TAS
• [x] SPBC21H7.03c acid phosphatase
• [x] SPCC297.05 -> reg endosome-vac
• [x] ulp2 SPAC17A5.07c

rearranged

• [ ] SPAC212.06c DNA helicase in rearranged telomeric region, truncated
• [ ] SPAC977.04 truncated C terminal region of membrane transporter
• [ ] SPAC186.04c N-terminal of transmembrane channel, truncated

my big rock for tomorrow....

[ValWood]

Jacky has never heard of tea5 either. I can't find anything in my e-mail archive about this name. For now I will change this to an obsolete name and revert to "conserved unknown"

[Antonialock]

Looks like tea5 was named by the Chang lab? https://www.google.co.uk/url?sa=t&rct=j&q=&esrc=s&source=web&cd=11&cad=rja&uact=8&ved=0ahUKEwjR6aOq5JPVAhWPb1AKHQ7_DIU4ChAWCCMwAA&url=https%3A%2F%2Facademiccommons.columbia.edu%2Fdownload%2Ffedora_content%2Fdownload%2Fac%3A206020%2FCONTENT%2FLutz_columbia_0054D_12454.pdf&usg=AFQjCNHCvEU6HOCaBUyATDs-Qu_XeNLl6A

"Based upon its properties described below we named this gene tea5 (tip elongation aberrant 5). The amino acid sequence of tea5p is predicted to have a kinase domain with sequence variations in its active site, suggesting it is a pseudokinase."

also in this pub https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5011436/

[ValWood]

Good detective work. I'll give it some sort of high level polarity annotation for now with a TAS to Fulvia's paper...I'll call it a kinase until anything is published to the contrary...

[ValWood]

curated PMID:24818994 for ulp2