MATPredict · mating-type report

KbestiolaeCBS10118

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 02:04 UTC by MATPredict 0.8.1

Result

Mating type

alphahigh confidence

Called loci 1

alpha MAT family · Basidiomycota

high confidence
Gene order of the alpha locus on KI894020alpha locus: genes from left to right on KI894020, 1,933,744 to 1,992,737: RPL39 (core MAT gene, plus strand); STE3 (core MAT gene, minus strand); MFa (core MAT gene, minus strand); MFalpha (core MAT gene, minus strand); PAN6 (conserved flank, minus strand).1,940 kb1,950 kb1,960 kb1,970 kb1,980 kb1,990 kb1,426.6 kb more to contig end →called locusRPL39: core MAT gene, 1,933,744–1,933,993 (+), identity 90.2%, gene modelRPL39STE3: core MAT gene, 1,951,779–1,952,710 (-), identity 54.2%, search hit onlySTE3MFa: core MAT gene, 1,961,844–1,961,960 (-), identity 47.619%, search hit onlyMFa (lost to MFalpha)MFalpha: core MAT gene, 1,961,844–1,961,960 (-), identity 60.53%, gene modelMFalphaPAN6: conserved flank, 1,991,126–1,992,737 (-), identity 63.7%, search hit onlyPAN6
Gene order on KI894020. Scroll sideways to see the whole figure.
FungiDB release 68 gene models on KI894020, 1,930,798 to 1,995,685I302_04107 1,929,318-1,932,351 (-): hypothetical proteinI302_04107I302_04108 1,934,497-1,938,088 (-): hypothetical proteinI302_04108I302_04109 1,938,473-1,940,813 (-): kinetochore protein NDC80I302_04109I302_04110 1,941,198-1,943,637 (-): STE/STE20/PAKA protein kinaseI302_04110I302_04111 1,944,106-1,948,593 (-): hypothetical proteinI302_04111I302_04112 1,949,146-1,951,666 (+): E1-like protein-activating enzyme Gsa7p/Apg7pI302_04112I302_04113 1,951,779-1,952,710 (-): hypothetical proteinI302_04113I302_04114 1,953,730-1,956,945 (+): hypothetical proteinI302_04114I302_04115 1,957,049-1,958,546 (-): pre-60S factor REI1I302_04115I302_04116 1,958,918-1,961,518 (+): ATP-dependent RNA helicase DBP10I302_04116I302_04117 1,962,876-1,965,728 (-): hypothetical proteinI302_04117I302_04118 1,966,041-1,967,260 (-): hypothetical proteinI302_04118I302_04119 1,968,280-1,975,458 (+): chitin synthaseI302_04119I302_04120 1,976,122-1,978,871 (-): ATPaseI302_04120I302_04121 1,979,206-1,981,778 (+): hypothetical proteinI302_04121I302_04122 1,982,897-1,983,383 (+): hypothetical proteinI302_04122I302_04123 1,985,720-1,988,566 (+): hypothetical proteinI302_04123I302_04124 1,989,084-1,990,592 (+): hypothetical proteinI302_04124I302_04125 1,991,126-1,992,737 (-): pantoate-beta-alanine ligaseI302_04125I302_04126 1,993,203-1,995,633 (+): U4/U6 small nuclear ribonucleoprotein PRP4I302_04126
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
  • gene model
  • search hit only
  • MFa is a weak hit to the other idiomorph's gene and was not counted against the call.
Location
KI894020:1,933,744–1,992,737 · 59.0 kb
Own genes
KI894020:1,933,744–1,992,737 · 59.0 kb
Locus
Complete locus: MAT gene(s) with their flanking genes.
Genes modelled
4 of 5 gene hits
Nearest contig end
1.4 Mb
Region (samtools)
KI894020:1933744-1992737
Idiomorph scores
  • alpha 51.2

Margin over the set-aside MFa hit: 11.4 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
MFalpha59.0MFa47.6100.0higher identity

Gene evidence

GeneRoleModel Identity %E-value Position (strand)Exons Reference recordFungiDB gene
RPL39core MATgene modelexonerate90.2cov 100.0%5.0e-1768 bits1,933,744–1,933,993 +240410_jec20_MAT_anone
STE3core MAThit onlyDIAMOND, proteome54.2cov 71.3%3.8e-100288 bits1,951,779–1,952,710 -–40410_jec21_MAT_alphaI302_04113
MFacore MATother idiomorph, not countedlost to MFalpha, not countedhit onlytblastn47.6cov 100.0%4.7e-0537 bits1,961,844–1,961,960 -–40410_jec20_MAT_anone
MFalphacore MATgene modelexonerate60.5cov 100.0%3.9e-1051 bits1,961,844–1,961,960 -140410_jec21_MAT_alphanone
PAN6conserved flankhit onlyDIAMOND, proteome63.7cov 95.6%6.9e-170470 bits1,991,126–1,992,737 -–40410_jec20_MAT_aI302_04125
FAO1expected, not found–
NOG2not searchable: no reference protein in the database–
UAP1not searchable: no reference protein in the database–

Withheld candidate loci 3

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 (3).

Show the 3 withheld loci

Withheld loci (3)

familylocationidiomorph genesmodelledreason
MATKI894022:2,030,614–2,046,434alphaFAO1, SXI1, SXI23too few of the family's genes found
MATKI894024:1,643,449–1,644,879undeterminedFAO11too few of the family's genes found
MATKV700382:652,599–654,418undeterminedSTE31too few of the family's genes found

Provenance

Genome file
KbestiolaeCBS10118.genome.fasta
Assembly
12 contigs · 24.4 Mb · N50 3.4 Mb
Genome SHA-256
db1aa6f838b5bff6d0d42171fd78f73199fe39e390d92ee782c52aeefc59f368
MATPredict
0.8.1 (v0.8.1, 3a62e6302b)
Database
86f18d232e4fe95d · 185 records
Taxonomy
local NCBI taxonomy snapshot 2026-10-01
Parameters
phylum=Basidiomycota, phylum_guess={'requested': 'auto', 'status': 'ok', 'usable': True, 'reason': None, 'phylum': 'Basidiomycota', 'phylum_taxid': 5204, 'deepest_rank': 'species', 'routing_taxid': 1884633, '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 Basidiomycota', 'action': 'routed', 'weak_call_accepted': False, 'genetic_code': 1, 'genetic_code_from': 'family taxid 1884633', 'routed_by': 'family taxid 1884633 (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, supported_min_bitscore=33.0
Run started
2026-11-07T02:03:29Z
Run time
35 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