MATPredict · mating-type report

KmarxianusDMKU3-1042

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 02:46 UTC by MATPredict 0.8.1

Result

Mating-type loci

MATalphahigh confidenceMATahigh confidenceMATahigh confidence

Called loci 3

MATalpha MATsc family · Ascomycota

high confidence
Gene order of the MATalpha locus on AP012213MATalpha locus: genes from left to right on AP012213, 34,715 to 37,056: sla2 (conserved flank, plus strand); MATALPHA1 (core MAT gene, minus strand); MATA2 (core MAT gene, plus strand); MATALPHA2 (core MAT gene, plus strand).34.5 kb35.0 kb35.5 kb36.0 kb36.5 kb37.0 kb← 34.4 kb more to contig endcalled locussla2: conserved flank, 34,715–35,272 (+), identity 82.2%, search hit onlysla2MATALPHA1: core MAT gene, 35,333–36,112 (-), identity 52.5%, search hit onlyMATALPHA1MATA2: core MAT gene, 36,379–37,056 (+), identity 34.9%, search hit onlyMATA2 (lost to MATALPHA2)MATALPHA2: core MAT gene, 36,379–37,056 (+), identity 36.7%, search hit onlyMATALPHA2
Gene order on AP012213. Scroll sideways to see the whole figure.
FungiDB release 71 gene models on AP012213, 34,415 to 37,356KLMA_10013 34,715-35,272 (+): XM_022818140.1KLMA_10013KLMA_10014 35,333-36,112 (-): mating-type protein ALPHA1KLMA_10014 MATALPHA1KLMA_10015 36,379-37,056 (+): mating-type protein ALPHA2KLMA_10015 HMLALPHA2
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
  • MATA2 is a weak hit to the other idiomorph's gene and was not counted against the call.
Location
AP012213:34,715–37,056 · 2.3 kb
Cross-lineage class
MAT1-1
Own genes
AP012213:34,715–37,056 · 2.3 kb
Locus
Complete locus: MAT gene(s) with their flanking genes.
Genes modelled
3 of 4 gene hits
Nearest contig end
34.7 kb
Region (samtools)
AP012213:34715-37056
Idiomorph scores
  • MATalpha 273.0

Margin over the set-aside MATA2 hit: 1.8 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
MATALPHA236.7MATA234.9100.0higher identity

Gene evidence

GeneRoleModel Identity %E-value Position (strand)Exons Reference recordFungiDB gene
sla2conserved flankhit onlyDIAMOND, proteome82.2cov 30.1%1.5e-95281 bits34,715–35,272 +–28985_nrrl-y-1140_MATsc_MATaKLMA_10013
MATALPHA1core MAThit onlyDIAMOND, proteome52.5cov 100.0%3.7e-96273 bits35,333–36,112 -–28985_nrrl-y-1140_MATsc_HMLalphaKLMA_10014 MATALPHA1
MATA2core MATother idiomorph, not countedlost to MATALPHA2, not countedhit onlyDIAMOND, proteome34.9cov 71.4%1.6e-1663 bits36,379–37,056 +–4932_s288c_MATsc_HMRaKLMA_10015 HMLALPHA2
MATALPHA2core MAThit onlyDIAMOND, proteome36.7cov 40.0%1.4e-36118 bits36,379–37,056 +–4956_da2_MATsc_MATalphaKLMA_10015 HMLALPHA2
cha1not searchable: no reference protein in the database–

MATa MATsc family · Ascomycota

high confidence
Gene order of the MATa locus on AP012213MATa locus: genes from left to right on AP012213, 290,215 to 294,626: sla2 (conserved flank, plus strand); MATA1 (core MAT gene, minus strand); MATA2 (core MAT gene, plus strand).290 kb291 kb292 kb293 kb294 kb← 289.9 kb more to contig endcalled locussla2: conserved flank, 290,215–292,332 (+), identity 64.6%, search hit onlysla2MATA1: core MAT gene, 292,355–292,996 (-), identity 47.2%, search hit onlyMATA1MATA2: core MAT gene, 293,862–294,626 (+), identity 53.3%, search hit onlyMATA2
Gene order on AP012213. Scroll sideways to see the whole figure.
FungiDB release 71 gene models on AP012213, 289,915 to 294,926KLMA_10141 290,215-292,332 (+): SLA2KLMA_10141 SLA2KLMA_10142 292,355-292,996 (-): MATA1KLMA_10142 MATA1KLMA_10143 293,862-294,626 (+): mating-type protein A2KLMA_10143 MATA2KLMA_10144 294,677-298,795 (-): LAA1KLMA_10144 LAA1
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
AP012213:290,215–294,626 · 4.4 kb
Cross-lineage class
MAT1-2
Own genes
AP012213:290,215–294,626 · 4.4 kb
Locus
Complete locus: MAT gene(s) with their flanking genes.
Genes modelled
3 of 3 gene hits
Nearest contig end
290.2 kb
Region (samtools)
AP012213:290215-294626
Idiomorph scores
  • MATa 120.0

No other idiomorph scored.

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

Gene evidence

GeneRoleModel Identity %E-value Position (strand)Exons Reference recordFungiDB gene
sla2conserved flankhit onlyDIAMOND, proteome64.6cov 100.0%8.3e-289796 bits290,215–292,332 +–28985_nrrl-y-1140_MATsc_MATaKLMA_10141 SLA2
MATA1core MAThit onlyDIAMOND, proteome47.2cov 42.1%2.8e-37120 bits292,355–292,996 -–4932_s288c_MATsc_HMRaKLMA_10142 MATA1
MATA2core MAThit onlyDIAMOND, proteome53.3cov 100.0%1.1e-85246 bits293,862–294,626 +–28985_nrrl-y-1140_MATsc_MATaKLMA_10143 MATA2
cha1not searchable: no reference protein in the database–

MATa MATsc family · Ascomycota

high confidence
Gene order of the MATa locus on AP012215MATa locus: genes from left to right on AP012215, 61,549 to 64,163: MATA2 (core MAT gene, minus strand); MATA1 (core MAT gene, plus strand); sla2 (conserved flank, minus strand).61.5 kb62.0 kb62.5 kb63.0 kb63.5 kb64.0 kb← 61.2 kb more to contig endcalled locusMATA2: core MAT gene, 61,549–62,313 (-), identity 53.3%, search hit onlyMATA2MATA1: core MAT gene, 63,179–63,820 (+), identity 47.2%, search hit onlyMATA1sla2: conserved flank, 63,843–64,163 (-), identity 96.4%, search hit onlysla2
Gene order on AP012215. Scroll sideways to see the whole figure.
FungiDB release 71 gene models on AP012215, 61,249 to 64,463KLMA_30020 60,293-61,498 (+): AP-1 accessory protein LAA1KLMA_30020KLMA_30021 61,549-62,313 (-): mating-type protein A2KLMA_30021 MATA2KLMA_30022 63,179-63,820 (+): mating-type protein A1KLMA_30022 MATA1KLMA_30023 63,843-64,163 (-): protein SLA2KLMA_30023
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
AP012215:61,549–64,163 · 2.6 kb
Cross-lineage class
MAT1-2
Own genes
AP012215:61,549–64,163 · 2.6 kb
Locus
Complete locus: MAT gene(s) with their flanking genes.
Genes modelled
3 of 3 gene hits
Nearest contig end
61.5 kb
Region (samtools)
AP012215:61549-64163
Idiomorph scores
  • MATa 120.0

No other idiomorph scored.

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

Gene evidence

GeneRoleModel Identity %E-value Position (strand)Exons Reference recordFungiDB gene
MATA2core MAThit onlyDIAMOND, proteome53.3cov 100.0%1.1e-85246 bits61,549–62,313 -–28985_nrrl-y-1140_MATsc_MATaKLMA_30021 MATA2
MATA1core MAThit onlyDIAMOND, proteome47.2cov 42.1%2.8e-37120 bits63,179–63,820 +–4932_s288c_MATsc_HMRaKLMA_30022 MATA1
sla2conserved flankhit onlyDIAMOND, proteome96.4cov 16.4%1.8e-64196 bits63,843–64,163 -–28985_nrrl-y-1140_MATsc_MATaKLMA_30023
cha1not searchable: no reference protein in the database–

Withheld candidate loci 26

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: fewer than 2 genes could be modelled (26).

Show the 26 withheld loci

Withheld loci (26)

familylocationidiomorph genesmodelledreason
MATscAP012213:111,060–111,218MATalphaMATALPHA10fewer than 2 genes could be modelled
MATscAP012215:725,159–725,314undeterminedMATALPHA20fewer than 2 genes could be modelled
MATscAP012215:752,338–752,490MATalphaMATALPHA10fewer than 2 genes could be modelled
MATscAP012215:1,036,110–1,036,307MATaMATA10fewer than 2 genes could be modelled
MATscAP012215:1,473,359–1,473,526undeterminedMATALPHA20fewer than 2 genes could be modelled
MATscAP012219:14,427–14,591MATalphaMATALPHA10fewer than 2 genes could be modelled
MATscAP012219:71,840–71,944undeterminedMATALPHA20fewer than 2 genes could be modelled
MATscAP012219:196,606–196,827MATalphaMATALPHA10fewer than 2 genes could be modelled
MATscAP012219:293,113–293,286MATalphaMATALPHA10fewer than 2 genes could be modelled
MATscAP012219:603,379–603,519undeterminedMATALPHA20fewer than 2 genes could be modelled
MATscAP012219:704,566–704,757MATaMATA10fewer than 2 genes could be modelled
MATscAP012216:145,429–145,590undeterminedMATALPHA20fewer than 2 genes could be modelled
MATscAP012216:709,525–709,620MATaMATA10fewer than 2 genes could be modelled
MATscAP012216:1,100,940–1,119,276undeterminedMATALPHA20fewer than 2 genes could be modelled
MATscAP012216:1,308,527–1,308,706undeterminedMATALPHA20fewer than 2 genes could be modelled
MATscAP012214:607,348–607,497MATalphaMATALPHA10fewer than 2 genes could be modelled
MATscAP012214:1,370,907–1,371,068MATaMATA10fewer than 2 genes could be modelled
MATscAP012218:16,161–16,358undeterminedMATALPHA20fewer than 2 genes could be modelled
MATscAP012218:291,860–292,288MATalphaMATALPHA10fewer than 2 genes could be modelled
MATscAP012218:1,139,060–1,139,155undeterminedMATALPHA20fewer than 2 genes could be modelled
MATscAP012217:127,016–127,171undeterminedMATALPHA20fewer than 2 genes could be modelled
MATscAP012217:224,525–224,662MATaMATA10fewer than 2 genes could be modelled
MATscAP012217:510,811–511,029MATalphaMATALPHA10fewer than 2 genes could be modelled
MATscAP012217:694,120–694,224undeterminedMATALPHA20fewer than 2 genes could be modelled
MATscAP012217:729,821–729,958MATalphaMATALPHA10fewer than 2 genes could be modelled
MATscAP012217:906,817–906,912MATaMATA10fewer than 2 genes could be modelled

Provenance

Genome file
KmarxianusDMKU3-1042.genome.fasta
Assembly
9 contigs · 11.0 Mb · N50 1.4 Mb
Genome SHA-256
1f66aa7001d2e8a86b99257cc4b8cc9873f89bee17d99b9fa77ab3da8a77ade2
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': 4893, '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 4893', 'routed_by': 'family taxid 4893 (direct)'}, 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
2026-11-07T02:45:57Z
Run time
12 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