MATPredict · mating-type report

PnodorumSN15

MAT locus above the FungiDB annotation (gene by gene)

organism not recorded

Run by MATPredict 0.8.1 (v0.8.1, 3a62e6302b) · database 86f18d232e4f · local NCBI taxonomy snapshot 2026-10-01 · rendered 2026-11-07 02:55 UTC by MATPredict 0.8.1

Result

Mating type

MAT1-1high confidence

Called loci 1

MAT1-1 MAT family · Ascomycota

high confidence
Gene order of the MAT1-1 locus on CP069023MAT1-1 locus: genes from left to right on CP069023, 1,879,443 to 1,902,705: MAT1-1-1 (core MAT gene, plus strand); APN2 (conserved flank, minus strand); COX13 (conserved flank, plus strand); MAT1-2-1 (core MAT gene, minus strand); MAT1-1-4 (core MAT gene, minus strand).1,880 kb1,885 kb1,890 kb1,895 kb1,900 kb1,643.4 kb more to contig end →called locusMAT1-1-1: core MAT gene, 1,879,443–1,880,532 (+), identity 100.0%, search hit onlyMAT1-1-1APN2: conserved flank, 1,883,819–1,885,776 (-), identity 88.6%, search hit onlyAPN2COX13: conserved flank, 1,886,092–1,886,702 (+), identity 51.6%, search hit onlyCOX13MAT1-2-1: core MAT gene, 1,900,089–1,900,262 (-), identity 27.586%, search hit onlyMAT1-2-1 (lost to MAT1-1-1)MAT1-1-4: core MAT gene, 1,902,598–1,902,705 (-), identity 39.474%, search hit onlyMAT1-1-4
Gene order on CP069023. Scroll sideways to see the whole figure.
FungiDB release 71 gene models on CP069023, 1,878,279 to 1,903,870JI435_003740 1,877,758-1,878,708 (+): Pyridoxamine 5'-phosphate oxidase | domain-containing proteinJI435_003740JI435_003750 1,879,443-1,880,532 (+): mating-type protein MAT-1JI435_003750JI435_400630 1,883,316-1,883,569 (+): unspecified productJI435_400630JI435_003770 1,883,819-1,885,776 (-): DNA-(apurinic or apyrimidinic site) endonuclease 2JI435_003770JI435_003780 1,886,092-1,886,702 (+): cytochrome c oxidase subunitJI435_003780JI435_003790 1,886,895-1,889,351 (-): Anaphase-promoting complex subunit 5 | domain-containing proteinJI435_003790JI435_003810 1,889,681-1,890,554 (-): Complex I intermediate-associated protein 30 (CIA30) | domain-containing proteinJI435_003810JI435_003820 1,890,856-1,892,107 (+): Mitochondrial carrier protein | domain-containing proteinJI435_003820JI435_003840 1,892,644-1,893,806 (+): unspecified productJI435_003840JI435_003850 1,894,200-1,894,743 (-): translation machinery-associated protein 22JI435_003850JI435_003870 1,895,349-1,896,114 (-): PAT complex subunit Asterix | domain-containing proteinJI435_003870JI435_003880 1,896,660-1,901,743 (+): mediator of RNA polymerase II transcription subunit 12JI435_003880JI435_003890 1,902,142-1,903,308 (-): unspecified productJI435_003890JI435_300220 1,903,587-1,905,189 (-): Autophagy-related protein 29JI435_300220
FungiDB release 71 annotation of the same window: gene models from the GFF (filled = CDS, pale = UTR exon, line = intron, arrow = strand). Green genes overlap a MATPredict gene on the same strand; grey genes do not. Click a gene to open it on fungidb.org.
  • core MAT gene
  • conserved flank
  • search hit only
  • MAT1-2-1 is a weak hit to the other idiomorph's gene and was not counted against the call.
Location
CP069023:1,879,443–1,902,705 · 23.3 kb
Own genes
CP069023:1,879,443–1,902,705 · 23.3 kb
Locus
Complete locus: MAT gene(s) with their flanking genes.
Genes modelled
3 of 5 gene hits
Nearest contig end
1.6 Mb
Region (samtools)
CP069023:1879443-1902705
Idiomorph scores
  • MAT1-1 682.0
  • MAT1-2 33.1

Margin over the next idiomorph: 648.9

Score: bitscore of the best core-gene hit for each idiomorph.

Overlapping hits resolved

Where genes of two idiomorphs hit the same place, the stronger hit was kept.

keptidentity %set asideidentity %overlap %basis
MAT1-1-1100.0MAT1-2-125.7100.0higher identity

Gene evidence

GeneRoleModel Identity %E-value Position (strand)Exons Reference recordFungiDB gene
MAT1-1-1core MAThit onlyDIAMOND, proteome100.0cov 100.0%8.9e-254682 bits1,879,443–1,880,532 +–13684_sn435pl98_MAT_MAT1-1JI435_003750
APN2conserved flankhit onlyDIAMOND, proteome88.6cov 36.7%9.7e-228640 bits1,883,819–1,885,776 -–2903220_liq80xsp_MAT_combinedJI435_003770
COX13conserved flankhit onlyDIAMOND, proteome51.6cov 70.2%3.6e-40124 bits1,886,092–1,886,702 +–5158_cbs114723_MAT_unswitchedJI435_003780
MAT1-2-1core MATother idiomorph, not countedlost to MAT1-1-1, not countedhit onlytblastn27.6cov 37.0%7.2e-0233 bits1,900,089–1,900,262 -–27337_tv103_MAT_MAT1-2JI435_003880 (opposite strand)
MAT1-1-4core MAThit onlytblastn39.5cov 15.0%2.5e-0133 bits1,902,598–1,902,705 -–199306_rmscc1040_MAT_MAT1-1JI435_003890
SLA2expected, not found–

Withheld candidate loci 3

Places with some MAT-gene evidence that did not pass a quality gate. Most genomes have several. They are listed so a known locus can be checked against them, not because they are likely calls.

Reasons: too few of the family's genes found (2); fewer than 2 genes could be modelled (1).

Show the 3 withheld loci

Withheld loci (3)

familylocationidiomorph genesmodelledreason
MATCP069023:2,570,931–2,578,432MAT1-1MAT1-1-1, SLA21fewer than 2 genes could be modelled
MATCP069026:1,550,061–1,552,258MAT1-2MAT1-2-11too few of the family's genes found
MATCP069032:690,986–699,835MAT1-2MAT1-1-1, MAT1-2-11too few of the family's genes found

Provenance

Genome file
PnodorumSN15.genome.fasta
Assembly
23 contigs · 37.0 Mb · N50 1.7 Mb
Genome SHA-256
d8de9b95f93f6741a75180ee4c7ded1d5d76e096a2d438f2cffad43afcb08b2b
MATPredict
0.8.1 (v0.8.1, 3a62e6302b)
Database
86f18d232e4fe95d · 185 records
Taxonomy
local NCBI taxonomy snapshot 2026-10-01
Parameters
phylum=Ascomycota, phylum_guess={'requested': 'auto', 'status': 'ok', 'usable': True, 'reason': None, 'phylum': 'Ascomycota', 'phylum_taxid': 4890, 'deepest_rank': 'genus', 'routing_taxid': 5020, 'routing_taxid_rank': 'family', 'flags': [], 'gmg_version': 'gmg 0.3.2 (66055154a)', 'index': 'bfd-reps-2026.10.5-s20000.gmgi', 'index_sha256': '0f319567f1cab17643e1daf7ffdc0e3b312bd43913e351568108d67a4a19702c', 'index_spec': 'bfd-reps-2026.10.5-s20000.gmgi', 'note': 'GmG called phylum Ascomycota', 'action': 'routed', 'weak_call_accepted': False, 'genetic_code': 1, 'genetic_code_from': 'family taxid 5020', 'routed_by': 'family taxid 5020 (lineage)'}, genetic_code=1, min_hits=2, require_core_role=True, max_polished_clusters_per_family=6, polish_strong_identity=50.0, polish_core_pair=True, partial_core_policy=off, homothallic_policy=off, confidence_cap_policy=off, cross_family_policy=off, fallback_after_withheld_policy=off, strong_single_gene_policy=off, scoped_roster_policy=off, scoped_roster=off: BGL1,GAP1 not searched, supported_min_bitscore=33.0
Run started
2026-11-07T02:53:57Z
Run time
78 s
Files
detection_report.yaml, detected_loci.gff3

Cite MATPredict as given in CITATION.cff at github.com/stajichlab/MATPredict. The reference records named in the gene tables are curated database entries; each record's metadata cites its source publication.

How to read this report

Idiomorph
The form of the mating-type locus a strain carries (for example MAT1-1 or MAT1-2, Plus or Minus). Basidiomycota HD and PR alleles are named after the reference they match.
High confidence
Every expected core MAT gene was found and modelled, with a conserved flanking gene where the family has one, on one contig.
Medium confidence
The core genes were found, but a gene could not be modelled, no conserved flank was found, or the locus is split (one step down).
Low confidence
A single isolated gene hit, or no core MAT gene.
Model status
Gene model: the reference protein was aligned to the genome to build the gene (exonerate, miniprot). Models differ: the two tools disagree on the structure; the alternate model is shown. Hit only: a search hit with no model, weaker evidence.
Identity
Percent amino-acid identity between the gene (or hit) and the closest reference protein.
Reference record
The curated database record whose protein matched best. Each record's metadata cites the publication or deposit it comes from.

Limits