MATPredict · mating-type report

PbrasiliensisPb18

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 02:37 UTC by MATPredict 0.8.1

Result

Mating type

MAT1-2medium confidence

Called loci 1

MAT1-2 MAT family · Ascomycota

medium confidence
Gene order of the MAT1-2 locus on KN275963MAT1-2 locus: genes from left to right on KN275963, 1,332,301 to 1,354,008: APN2 (conserved flank, minus strand); COX13 (conserved flank, plus strand); MAT1-1-4 (core MAT gene, plus strand); MAT1-1-3 (core MAT gene, minus strand); MAT1-2-1 (core MAT gene, minus strand); CIMG_00407 (core MAT gene, plus strand); MAT1-2-4 (core MAT gene, plus strand); SLA2 (conserved flank, minus strand).1,335 kb1,340 kb1,345 kb1,350 kb1,355 kb155.8 kb more to contig end →called locusAPN2: conserved flank, 1,332,301–1,334,449 (-), identity 77.1%, search hit onlyAPN2COX13: conserved flank, 1,334,887–1,335,593 (+), identity 79.0%, search hit onlyCOX13MAT1-1-4: core MAT gene, 1,339,152–1,343,457 (+), identity 54.65%, the two modelling tools disagreeMAT1-1-4MAT1-1-3: core MAT gene, 1,344,727–1,345,826 (-), identity 35.1%, search hit onlyMAT1-1-3 (lost to MAT1-2-1)MAT1-2-1: core MAT gene, 1,344,727–1,345,826 (-), identity 51.8%, search hit onlyMAT1-2-1CIMG_00407: core MAT gene, 1,346,337–1,347,258 (+), identity 30.6%, search hit onlyCIMG_00407MAT1-2-4: core MAT gene, 1,346,754–1,346,864 (+), identity 35.135%, search hit onlyMAT1-2-4SLA2: conserved flank, 1,349,640–1,354,008 (-), identity 88.7%, search hit onlySLA2
Gene order on KN275963. Scroll sideways to see the whole figure.
FungiDB release 71 gene models on KN275963, 1,331,215 to 1,355,092PADG_06115 1,332,301-1,334,449 (-): DNA-(apurinic or apyrimidinic site) endonuclease 2PADG_06115PADG_06116 1,334,887-1,335,593 (+): Cytochrome c oxidase subunit VIa | domain-containing proteinPADG_06116PADG_06117 1,336,444-1,337,471 (+): hypothetical proteinPADG_06117PADG_06118 1,344,727-1,345,826 (-): HMG (high mobility group) box | domain-containing proteinPADG_06118PADG_06119 1,346,337-1,347,258 (+): hypothetical proteinPADG_06119PADG_06120 1,349,640-1,354,008 (-): I/LWEQ domain | ANTH domain | domain-containing proteinPADG_06120
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
  • tools disagree
  • alternate model
  • search hit only
Location
KN275963:1,332,301–1,354,008 · 21.7 kb
Own genes
KN275963:1,332,301–1,354,008 · 21.7 kb
Locus
Complete locus: MAT gene(s) with their flanking genes.
Genes modelled
6 of 8 gene hits
Nearest contig end
156.9 kb
Region (samtools)
KN275963:1332301-1354008
Idiomorph scores
  • MAT1-2 278.0
  • MAT1-1 120.0

Margin over the next idiomorph: 158.0

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
MAT1-2-151.8MAT1-1-335.1100.0higher identity

Gene evidence

GeneRoleModel Identity %E-value Position (strand)Exons Reference recordFungiDB gene
APN2conserved flankhit onlyDIAMOND, proteome77.1cov 29.2%2.9e-243679 bits1,332,301–1,334,449 -–2903220_liq80xsp_MAT_combinedPADG_06115
COX13conserved flankhit onlyDIAMOND, proteome79.0cov 71.4%1.1e-46140 bits1,334,887–1,335,593 +–199306_rmscc1040_MAT_MAT1-1PADG_06116
MAT1-1-4core MATmodels differexonerateminiprot: 1,338,861–1,339,418, 36.9%54.6cov 35.4%6.6e-31120 bits1,339,152–1,343,457 +2199306_rmscc1040_MAT_MAT1-1none
MAT1-1-3core MATlost to MAT1-2-1, not countedhit onlyDIAMOND, proteome35.1cov 41.1%1.5e-0949 bits1,344,727–1,345,826 -–230073_uamh-1363_MAT_MAT1-1PADG_06118
MAT1-2-1core MAThit onlyDIAMOND, proteome51.8cov 65.9%1.3e-94278 bits1,344,727–1,345,826 -–61372_suf959_MAT_MAT1-2PADG_06118
CIMG_00407core MAThit onlyDIAMOND, proteome30.6cov 89.0%2.7e-37125 bits1,346,337–1,347,258 +–5501_rs_MAT_MAT1-2PADG_06119
MAT1-2-4core MAThit onlytblastn35.1cov 15.0%4.7e-0132 bits1,346,754–1,346,864 +–746128_af293_MAT_MAT1-2PADG_06119
SLA2conserved flankhit onlyDIAMOND, proteome88.7cov 99.3%< 1e-1801,548 bits1,349,640–1,354,008 -–107463_unknown-1_MAT_MAT1-2PADG_06120
MAT1-1-1expected, not found–

Withheld candidate loci 2

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).

Show the 2 withheld loci

Withheld loci (2)

familylocationidiomorph genesmodelledreason
MATKN275958:1,479,442–1,481,817MAT1-2MAT1-2-11too few of the family's genes found
MATKN275959:1,948,785–1,950,363MAT1-2MAT1-2-11too few of the family's genes found

Provenance

Genome file
PbrasiliensisPb18.genome.fasta
Assembly
57 contigs · 30.0 Mb · N50 2.1 Mb
Genome SHA-256
2ee7b93edb2687e67be3c010b29a5804cc003a5bfaac685b1d03b2c3c68c5723
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': 299071, '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 299071', 'routed_by': 'family taxid 299071 (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
2026-11-07T02:36:18Z
Run time
68 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