MATPredict · mating-type report

TrubrumCBS118892

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 02:32 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 GG700649MAT1-1 locus: genes from left to right on GG700649, 2,170,556 to 2,181,729: CIMG_00407 (core MAT gene, minus strand); MAT1-2-4 (core MAT gene, minus strand); MAT1-1-1 (core MAT gene, minus strand); MAT1-1-4 (core MAT gene, minus strand); APN2 (conserved flank, minus strand); COX13 (conserved flank, plus strand); SLA2 (conserved flank, minus strand).2,170 kb2,172 kb2,174 kb2,176 kb2,178 kb2,180 kb2,182 kb776.8 kb more to contig end →called locusCIMG_00407: core MAT gene, 2,170,556–2,170,783 (-), identity 30.263%, search hit onlyCIMG_00407MAT1-2-4: core MAT gene, 2,170,673–2,170,864 (-), identity 32.812%, search hit onlyMAT1-2-4MAT1-1-1: core MAT gene, 2,171,481–2,172,684 (-), identity 50.6%, search hit onlyMAT1-1-1MAT1-1-4: core MAT gene, 2,173,394–2,174,662 (-), identity 41.8%, search hit onlyMAT1-1-4APN2: conserved flank, 2,175,427–2,177,519 (-), identity 76.6%, search hit onlyAPN2COX13: conserved flank, 2,177,761–2,178,413 (+), identity 68.8%, search hit onlyCOX13SLA2: conserved flank, 2,178,837–2,181,729 (-), identity 88.1%, search hit onlySLA2
Gene order on GG700649. Scroll sideways to see the whole figure.
FungiDB release 71 gene models on GG700649, 2,169,999 to 2,182,287TERG_02405 2,170,451-2,171,354 (-): hypothetical proteinTERG_02405TERG_02406 2,171,481-2,172,684 (-): Mating-type protein MAT alpha 1 HMG-box | domain-containing proteinTERG_02406TERG_02407 2,173,394-2,174,662 (-): hypothetical proteinTERG_02407TERG_02408 2,175,427-2,177,519 (-): DNA-(apurinic or apyrimidinic site) endonuclease 2TERG_02408TERG_02409 2,177,761-2,178,413 (+): Cytochrome c oxidase subunit VIa | domain-containing proteinTERG_02409TERG_02410 2,178,837-2,181,729 (-): ANTH domain | I/LWEQ domain | domain-containing proteinTERG_02410
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
  • CIMG_00407 is a weak hit to the other idiomorph's gene and was not counted against the call.
  • MAT1-2-4 is a weak hit to the other idiomorph's gene and was not counted against the call.
Location
GG700649:2,170,556–2,181,729 · 11.2 kb
Own genes
GG700649:2,170,556–2,181,729 · 11.2 kb
Locus
Complete locus: MAT gene(s) with their flanking genes.
Genes modelled
5 of 7 gene hits
Nearest contig end
777.4 kb
Region (samtools)
GG700649:2170556-2181729
Idiomorph scores
  • MAT1-1 309.0
  • MAT1-2 42.7

Margin over the next idiomorph: 266.3

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

Gene evidence

GeneRoleModel Identity %E-value Position (strand)Exons Reference recordFungiDB gene
CIMG_00407core MATother idiomorph, not countedhit onlytblastn30.3cov 21.0%1.5e-0442 bits2,170,556–2,170,783 -–5501_rs_MAT_MAT1-2TERG_02405
MAT1-2-4core MATother idiomorph, not countedhit onlytblastn32.8cov 26.0%1.1e-0443 bits2,170,673–2,170,864 -–746128_af293_MAT_MAT1-2TERG_02405
MAT1-1-1core MAThit onlyDIAMOND, proteome50.6cov 99.2%1.6e-105309 bits2,171,481–2,172,684 -–199306_rmscc1040_MAT_MAT1-1TERG_02406
MAT1-1-4core MAThit onlyDIAMOND, proteome41.8cov 68.7%9.3e-43140 bits2,173,394–2,174,662 -–199306_rmscc1040_MAT_MAT1-1TERG_02407
APN2conserved flankhit onlyDIAMOND, proteome76.6cov 90.4%3.4e-229641 bits2,175,427–2,177,519 -–27339_unknown-1_MAT_MAT1-2TERG_02408
COX13conserved flankhit onlyDIAMOND, proteome68.8cov 100.0%6.2e-59172 bits2,177,761–2,178,413 +–746128_af293_MAT_MAT1-2TERG_02409
SLA2conserved flankhit onlyDIAMOND, proteome88.1cov 99.3%< 1e-1801,224 bits2,178,837–2,181,729 -–107463_unknown-1_MAT_MAT1-2TERG_02410
MAT1-2-1expected, not found–

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
MATGG700656:517,125–536,955MAT1-2MAT1-2-1, MAT1-1-3, MAT1-2-101too few of the family's genes found

Provenance

Genome file
TrubrumCBS118892.genome.fasta
Assembly
36 contigs · 22.5 Mb · N50 2.2 Mb
Genome SHA-256
2904e2c21639249105a7bef4e51ef4cc1d6cb6b3e74d4faa26a8a53b3dd37329
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': 34384, '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 34384', 'routed_by': 'family taxid 34384 (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
2026-11-07T02:31:34Z
Run time
59 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