MATPredict · mating-type report

PbrasiliensisPb03

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 01:53 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 KN305539MAT1-2 locus: genes from left to right on KN305539, 1,302,065 to 1,320,427: 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).1,305 kb1,310 kb1,315 kb1,320 kb156.0 kb more to contig end →called locusAPN2: conserved flank, 1,302,065–1,303,654 (-), identity 71.1%, search hit onlyAPN2COX13: conserved flank, 1,304,651–1,305,357 (+), identity 79.0%, search hit onlyCOX13MAT1-1-4: core MAT gene, 1,308,049–1,309,846 (+), identity 38.3%, search hit onlyMAT1-1-4MAT1-1-3: core MAT gene, 1,311,666–1,312,765 (-), identity 35.1%, search hit onlyMAT1-1-3 (lost to MAT1-2-1)MAT1-2-1: core MAT gene, 1,311,666–1,312,765 (-), identity 51.8%, search hit onlyMAT1-2-1CIMG_00407: core MAT gene, 1,313,272–1,314,192 (+), identity 30.6%, search hit onlyCIMG_00407MAT1-2-4: core MAT gene, 1,313,689–1,313,799 (+), identity 35.135%, search hit onlyMAT1-2-4SLA2: conserved flank, 1,316,612–1,320,427 (-), identity 88.7%, search hit onlySLA2
Gene order on KN305539. Scroll sideways to see the whole figure.
FungiDB release 68 gene models on KN305539, 1,301,148 to 1,321,345PABG_05775 1,302,065-1,303,654 (-): hypothetical proteinPABG_05775PABG_05776 1,304,651-1,305,357 (+): hypothetical proteinPABG_05776PABG_12217 1,306,202-1,306,651 (+): hypothetical proteinPABG_12217PABG_12218 1,308,049-1,309,846 (+): hypothetical proteinPABG_12218PABG_05778 1,311,666-1,312,765 (-): hypothetical proteinPABG_05778PABG_05779 1,313,272-1,314,192 (+): hypothetical proteinPABG_05779PABG_05780 1,316,612-1,320,427 (-): hypothetical proteinPABG_05780PABG_05781 1,320,689-1,321,346 (+): hypothetical proteinPABG_05781
FungiDB release 68 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
Location
KN305539:1,302,065–1,320,427 · 18.4 kb
Own genes
KN305539:1,302,065–1,320,427 · 18.4 kb
Locus
Genes of both idiomorphs at one locus.
Genes modelled
6 of 8 gene hits
Nearest contig end
156.9 kb
Region (samtools)
KN305539:1302065-1320427
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, proteome71.1cov 86.5%2.3e-192545 bits1,302,065–1,303,654 -–27339_unknown-1_MAT_MAT1-2PABG_05775
COX13conserved flankhit onlyDIAMOND, proteome79.0cov 71.4%1.5e-46140 bits1,304,651–1,305,357 +–199306_rmscc1040_MAT_MAT1-1PABG_05776
MAT1-1-4core MAThit onlyDIAMOND, proteome38.3cov 67.9%3.7e-34120 bits1,308,049–1,309,846 +–199306_rmscc1040_MAT_MAT1-1PABG_12218
MAT1-1-3core MATlost to MAT1-2-1, not countedhit onlyDIAMOND, proteome35.1cov 41.1%1.5e-0949 bits1,311,666–1,312,765 -–230073_uamh-1363_MAT_MAT1-1PABG_05778
MAT1-2-1core MAThit onlyDIAMOND, proteome51.8cov 65.9%6.6e-95278 bits1,311,666–1,312,765 -–61372_suf959_MAT_MAT1-2PABG_05778
CIMG_00407core MAThit onlyDIAMOND, proteome30.6cov 89.0%2.7e-37125 bits1,313,272–1,314,192 +–5501_rs_MAT_MAT1-2PABG_05779
MAT1-2-4core MAThit onlytblastn35.1cov 15.0%4.6e-0132 bits1,313,689–1,313,799 +–746128_af293_MAT_MAT1-2PABG_05779
SLA2conserved flankhit onlyDIAMOND, proteome88.7cov 99.3%< 1e-1801,493 bits1,316,612–1,320,427 -–107463_unknown-1_MAT_MAT1-2PABG_05780
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
MATKN305531:1,962,328–1,963,906MAT1-2MAT1-2-11too few of the family's genes found
MATKN305534:1,360,284–1,362,664MAT1-2MAT1-2-11too few of the family's genes found

Provenance

Genome file
PbrasiliensisPb03.genome.fasta
Assembly
65 contigs · 29.1 Mb · N50 1.9 Mb
Genome SHA-256
46102db40c839f53aefbca08723ba66165e062e4214476302e3a615af25bf0a6
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': 'species', '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
2026-11-07T01:52:32Z
Run time
48 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