MATPredict · mating-type report

Pexpansumd1

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 02:44 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 JQFY01000238MAT1-1 locus: genes from left to right on JQFY01000238, 137,236 to 148,259: COX13 (conserved flank, minus strand); APN2 (conserved flank, plus strand); MAT1-1-1 (core MAT gene, plus strand); MAT1-2-1 (core MAT gene, plus strand); SLA2 (conserved flank, minus strand).138 kb140 kb142 kb144 kb146 kb148 kb128.2 kb more to contig end →called locusCOX13: conserved flank, 137,236–138,029 (-), identity 78.9%, search hit onlyCOX13APN2: conserved flank, 138,367–140,605 (+), identity 85.7%, search hit onlyAPN2MAT1-1-1: core MAT gene, 142,122–143,192 (+), identity 39.6%, search hit onlyMAT1-1-1MAT1-2-1: core MAT gene, 142,404–142,709 (+), identity 26.214%, search hit onlyMAT1-2-1 (lost to MAT1-1-1)SLA2: conserved flank, 144,393–148,259 (-), identity 89.5%, search hit onlySLA2
Gene order on JQFY01000238. Scroll sideways to see the whole figure.
FungiDB release 71 gene models on JQFY01000238, 136,686 to 148,810PEXP_003130 137,236-138,029 (-): Cytochrome c oxidase, subunit VIaPEXP_003130PEXP_003140 138,367-140,605 (+): Endonuclease/exonuclease/phosphatasePEXP_003140PEXP_003150 142,122-143,192 (+): Mating-type protein MAT alpha 1PEXP_003150PEXP_003160 144,393-148,259 (-): Epsin-like, N-terminalPEXP_003160
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
JQFY01000238:137,236–148,259 · 11.0 kb
Own genes
JQFY01000238:137,236–148,259 · 11.0 kb
Locus
Complete locus: MAT gene(s) with their flanking genes.
Genes modelled
4 of 5 gene hits
Nearest contig end
128.7 kb
Region (samtools)
JQFY01000238:137236-148259
Idiomorph scores
  • MAT1-1 99.0

Margin over the set-aside MAT1-2-1 hit: 13.4 identity points (the narrowest overlap resolution below).

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
MAT1-1-139.6MAT1-2-126.2100.0higher identity

Gene evidence

GeneRoleModel Identity %E-value Position (strand)Exons Reference recordFungiDB gene
COX13conserved flankhit onlyDIAMOND, proteome78.9cov 87.3%3.9e-71203 bits137,236–138,029 -–162425_fgsc-a4_MAT_combinedPEXP_003130
APN2conserved flankhit onlyDIAMOND, proteome85.7cov 29.2%1.3e-276764 bits138,367–140,605 +–2903220_liq80xsp_MAT_combinedPEXP_003140
MAT1-1-1core MAThit onlyDIAMOND, proteome39.6cov 35.5%8.6e-2699 bits142,122–143,192 +–199306_rmscc1040_MAT_MAT1-1PEXP_003150
MAT1-2-1core MATother idiomorph, not countedlost to MAT1-1-1, not countedhit onlytblastn26.2cov 30.0%1.1e-0134 bits142,404–142,709 +–578113_sxlc146_MAT_MAT1-2PEXP_003150
SLA2conserved flankhit onlyDIAMOND, proteome89.5cov 100.0%< 1e-1801,614 bits144,393–148,259 -–107463_unknown-1_MAT_MAT1-2PEXP_003160

Withheld candidate loci 1

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 (1).

Show the 1 withheld locus

Withheld loci (1)

familylocationidiomorph genesmodelledreason
MATJQFY01000227:822,072–823,735MAT1-2MAT1-2-11too few of the family's genes found

Provenance

Genome file
Pexpansumd1.genome.fasta
Assembly
270 contigs · 32.1 Mb · N50 360.6 kb
Genome SHA-256
4b67ee59a1b1fa13b61687a28af2991a0896d43b1f7a9a16ecec47f959026c87
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': 1131492, '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 1131492', 'routed_by': 'family taxid 1131492 (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
2026-11-07T02:43:41Z
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