MATPredict · mating-type report

TmentagrophytesTIMM2789

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 02:57 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 BFBS01016511MAT1-2 locus: genes from left to right on BFBS01016511, 55,408 to 67,922: CIMG_00407 (core MAT gene, minus strand); MAT1-2-4 (core MAT gene, minus strand); MAT1-1-3 (core MAT gene, plus strand); MAT1-2-1 (core MAT gene, plus strand); MAT1-1-4 (core MAT gene, minus strand); APN2 (conserved flank, minus strand); COX13 (conserved flank, plus strand); SLA2 (conserved flank, minus strand).56 kb58 kb60 kb62 kb64 kb66 kb68 kb← 54.8 kb more to contig endcalled locusCIMG_00407: core MAT gene, 55,408–56,046 (-), identity 25.352%, search hit onlyCIMG_00407MAT1-2-4: core MAT gene, 55,483–55,857 (-), identity 25.397%, search hit onlyMAT1-2-4MAT1-1-3: core MAT gene, 56,728–57,963 (+), identity 35.9%, search hit onlyMAT1-1-3 (lost to MAT1-2-1)MAT1-2-1: core MAT gene, 56,728–57,963 (+), identity 60.0%, search hit onlyMAT1-2-1MAT1-1-4: core MAT gene, 58,497–59,753 (-), identity 41.6%, search hit onlyMAT1-1-4APN2: conserved flank, 60,527–62,362 (-), identity 76.6%, search hit onlyAPN2COX13: conserved flank, 62,881–63,536 (+), identity 68.9%, search hit onlyCOX13SLA2: conserved flank, 63,961–67,922 (-), identity 88.1%, search hit onlySLA2
Gene order on BFBS01016511. Scroll sideways to see the whole figure.
FungiDB release 71 gene models on BFBS01016511, 54,784 to 68,547TMEN_9214 55,474-56,220 (-): unspecified productTMEN_9214TMEN_9215 56,728-57,963 (+): MAT+ sexual cell fertilization-promoting factorTMEN_9215TMEN_9216 58,497-59,753 (-): unspecified productTMEN_9216TMEN_9217 60,527-62,362 (-): DNA-(apurinic or apyrimidinic site) lyaseTMEN_9217TMEN_9218 62,881-63,536 (+): cytochrome c oxidase subunit 6ATMEN_9218TMEN_9219 63,961-67,922 (-): endocytosis proteinTMEN_9219TMEN_9220 68,455-71,160 (-): PH domain-containing proteinTMEN_9220
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
Location
BFBS01016511:55,408–67,922 · 12.5 kb
Own genes
BFBS01016511:55,408–67,922 · 12.5 kb
Locus
Genes of both idiomorphs at one locus.
Genes modelled
5 of 8 gene hits
Nearest contig end
55.4 kb
Region (samtools)
BFBS01016511:55408-67922
Idiomorph scores
  • MAT1-2 281.0
  • MAT1-1 127.0

Margin over the next idiomorph: 154.0

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
MAT1-2-160.0MAT1-1-335.9100.0higher identity

Gene evidence

GeneRoleModel Identity %E-value Position (strand)Exons Reference recordFungiDB gene
CIMG_00407core MAThit onlytblastn25.4cov 61.0%1.4e-1370 bits55,408–56,046 -–5501_rs_MAT_MAT1-2TMEN_9214
MAT1-2-4core MAThit onlytblastn25.4cov 42.0%9.6e-0646 bits55,483–55,857 -–746128_af293_MAT_MAT1-2TMEN_9214
MAT1-1-3core MATlost to MAT1-2-1, not countedhit onlyDIAMOND, proteome35.9cov 43.3%1.0e-1156 bits56,728–57,963 +–230073_uamh-1363_MAT_MAT1-1TMEN_9215
MAT1-2-1core MAThit onlyDIAMOND, proteome60.0cov 25.7%2.3e-95281 bits56,728–57,963 +–2903220_liq80xsp_MAT_combinedTMEN_9215
MAT1-1-4core MAThit onlyDIAMOND, proteome41.6cov 64.2%5.7e-38127 bits58,497–59,753 -–199306_rmscc1040_MAT_MAT1-1TMEN_9216
APN2conserved flankhit onlyDIAMOND, proteome76.6cov 90.4%1.3e-212598 bits60,527–62,362 -–27339_unknown-1_MAT_MAT1-2TMEN_9217
COX13conserved flankhit onlyDIAMOND, proteome68.9cov 100.0%2.2e-59173 bits62,881–63,536 +–5501_rs_MAT_MAT1-2TMEN_9218
SLA2conserved flankhit onlyDIAMOND, proteome88.1cov 99.3%< 1e-1801,531 bits63,961–67,922 -–107463_unknown-1_MAT_MAT1-2TMEN_9219
MAT1-1-1expected, 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
MATBFBS01016029:145,609–166,552MAT1-2MAT1-2-1, MAT1-2-101too few of the family's genes found

Provenance

Genome file
TmentagrophytesTIMM2789.genome.fasta
Assembly
16,543 contigs · 24.1 Mb · N50 81.1 kb
Genome SHA-256
42e32e15a4a5e2a4655a13bc1bac83dc11e559785a5553f4606cc657e78f495b
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
2026-11-07T02:56:33Z
Run time
67 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