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PMID:21933337 Risk assessment studies on succinate dehydrogenase inhibitors, the new weapons in the battle to control Septoria leaf blotch in wheat #207

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jingluodatacurator opened this issue Nov 21, 2023 · 74 comments

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approved archetype needs checking checked chemistry e.g. AE alteration in archetype FRAST new strain SdhB/C/D target site Uniprot id query

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jingluodatacurator commented Nov 21, 2023 •

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Curated by @jingluodatacurator

https://canto.phi-base.org/curs/fa6dafc2380a5876

Notes:
Uniprot IDs: G4XX47, G4XX53, G8EI90
~~Strains~~ Genes/proteins: SdhB, SdhC, SdhD (see Table 3 and Table 4)
Strains: IPO323 and IRE30
Main expt. for curation: see in Results 'Identification of Sdh mutations in carboxin-resistant
UV mutants' and 'Relationship between mutant Sdh variants and SDHI
sensitivity', and Table 3, Table 4, Figure 4.

Notes on Uniprot IDs:
basesd on GenBank accession numbers JF916683-916700 were given, G8EI90 was from JF916683 for SdhB, G4XX47 was from JF916689 for SdhD, G4XX53 was from JF916695 for SdhC.

jingluodatacurator self-assigned this

CuzickA added chemistry SdhB/C/D target site next needs_checking labels

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CuzickA added the needs new PHI-ECO terms label

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CuzickA added a commit to PHI-base/data that referenced this issue


          Add 'IRE30' to Zymoseptoria tritici strain list

e9723ab

PHI-base/curation#207

CuzickA commented Jan 16, 2024 •

edited

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AE alteration in archetype

Nichola's Table S4

SdhB(aaC137R)[Not assayed]
'C147R; SdhB; PYRNTE'

SdhB(aaS221T)[Not assayed]
'S231T; SdhB; PYRNTE'

SdhB(aaR265P)[Not assayed]
'R275P; SdhB; PYRNTE'

SdhB(aaH267F)[Not assayed]
'H277F; SdhB; PYRNTE'

SdhB(aaH267L)[Not assayed]
'H277L; SdhB; PYRNTE'

SdhB(aaH267N)[Not assayed]
'H277N; SdhB; PYRNTE'

SdhB(aaI269V)[Not assayed]
'H279V; SdhB; PYRNTE'

SdhB(aaS221P)[Not assayed]
'S231P; SdhB; PYRNTE'

SdhB(aaH267Y)[Not assayed]
'H277Y; SdhB; PYRNTE'

SdhB(aaS221P)[Not assayed]
'S231P; SdhB; PYRNTE'

SdhB(aaP155L, H267Y)[Not assayed]
Info from above for SdhB(aaH267Y)[Not assayed]
'H277Y; SdhB; PYRNTE'

Cannot find info for 'SdhB(aaP155L' In Nicola's S file or Mair et al 2016. Might need to use FRAST.

~~AE not added~~

Update 17_01_2024 FRAST done below. SdhB aaP155L (IRE30) 'P165L; SdhB; PYRNTE'
AE now added
SdhB(aaP155L, H267Y)[Not assayed] 'P165L, H277Y; SdhB; PYRNTE'

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CuzickA added Nearly ready for approval and removed needs PHI phenotype annotation labels

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CuzickA commented Jan 29, 2024 •

edited

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Next steps list

AC to follow up on the uniprot query for SdhB - might need changing UniProts now changed
AC to check AEs and queries with Nichola.
Once 1 and 2 done then the session will be ready to approve.

CuzickA added checked unapproved until archetype AE checked needs UniProt id swap and removed needs_checking next labels

CuzickA mentioned this issue

Decide what do to when curators use different UniProt ids for the same gene in different publications #125

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CuzickA mentioned this issue

PMID: 22536383 Mutagenesis and Functional Studies with Succinate Dehydrogenase Inhibitors in the Wheat Pathogen Mycosphaerella graminicola. #138

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jseager7 mentioned this issue

PMID:18992352 Identification of three mutant loci conferring carboxin-resistance and development of a novel transformation system in Aspergillus oryzae #173

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CuzickA commented May 13, 2024

Great, thanks @jseager7.

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CuzickA removed Nearly ready for approval needs UniProt id swap labels

CuzickA added approved and removed unapproved until archetype AE checked labels

CuzickA commented Sep 9, 2024

Session approved without Nichola checking AE alteration in archetype.

Closing ticket.

CuzickA closed this as completed

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