MAT.gene.search.rmd

Protein PGN.07108, which was detected during the CodingQuarry Pathogen Mode gene-calling, was identified as encoding mating-type protein MAT 1-1-1 by the EggNOG system. It is most similar to a mating-type protein from Gibberella monoliformis (8.5e-48), which causes “Maize ear and stalk rot”, in the same family as Geosmithia (Hypocreales).

note: all searches run on both original and PM proteins

1 EggNOG

EggNOG maintains several MAT Nog families (different from KEGG).

  • MAT 1-1-1, ENOG410YVGY

  • MAT 1-1-2, ENOG4110WT8

  • MAT 1-1-3, ENOG410XT0K

  • MAT 1-2-1, ENOG410XT0K

in the PM set, PGN.07108 was annotated at MAT 1-1-1

2 Mating type protein located

PGN.07108:

  • By DIAMOND search, aligns with uniprot protein 117187.FVEG_02491T0 to 8.5e-48
  • This was annotated based on placement in several MAT NOGs including the main MAT 1-1-1 family, ENOG410YVGY, a.k.a. 0YVGY@NOG
  • This was not picked up by KEGG or COG (making me suspect that EggNOG has its place in general annotation, should not ignore from now on!)

3 Protein Sequence


>PGN.07108
MATRSNLIERLSTASAADLLELLDDEPLFSLAARYFQRFPETNSGTFQSASQAKESIAEP
PKDKTKRPLNGFMAFRSYYMKIFPDVPQKSVSGFLTTLWNQDPFRNKWVLVAKVYSFIRD
EVGKDKIPLSQFLGISCPLMKIISPSAYLSTLGWRVDNQNEKGQHLVRFDPAASNNVADI
QLQNCPNTELDLLALVLDFGFLPAESFGLMQRMGANSNPIMTADTGNTTQHVVPCTIEKL
DFLYTVHKNPSKAAKDLLGEHYVDCIMQDSGYRVYDVQDLKQIDHISMVPPNEPSFYQYG
TTHAHFNMNKEPIFEISNIPDHRCYDISNSYDMDSIAGFVEPLGKYTYGFSDDSPPFSAH
NDFQLMF

4 Failed searches

4.1 KEGG ORTHOLOGY

The KEGG system contains two ortholog groups corresponding to mating type genes in fungi

mating-type protein A1: https://www.genome.jp/dbget-bin/www_bget?ko:K09358 (6 sequences) mating-type protein A2: https://www.genome.jp/dbget-bin/www_bget?ko:K09359 (6 sequences)

simply text-search the existing KEGG annotation locates no matches to either

These models are not very robust. KEGG is also very conservative in its estimations.

4.2 Orignial MAKER annotation

One of the genes is labelled as:

“augustus_masked-scaffold_9-processed-gene-0.321-mRNA-1_protein_Name:”Similar_to_swi10_Mating-type_switching_protein_swi10_(Schizosaccharomyces_pombe_(strain_972_/_ATCC_24843))“_AED:0.17_eAED:0.24_QI:0|-1|0|1|-1|1|1|0| "

It is not clear where this names comes from, as no other system identifies this as anything related to mating at all.

Eggnog found DIAMOND (similar to blastP) e-value similarity of “augustus_masked-scaffold_9-processed-gene-0.321-mRNA-1” to 5507.FOXG_05982P0 (uniprot), termed “DNA exision repair protein ERCC-1”. This general annotation is picked up also by InterProScan, pfam, PANTHER, and GO.

RWMurdoch

June 2, 2019