MATPredict · mating-type report

AthermomutatusHMRAF39

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 02:37 UTC by MATPredict 0.8.1

Result

Mating-type loci

MAT1-1high confidenceMAT1-2medium confidence

Called loci 2

MAT1-1 MAT family · Ascomycota

high confidence
Gene order of the MAT1-1 locus on NKHU02000077MAT1-1 locus: genes from left to right on NKHU02000077, 63,880 to 80,442: SLA2 (conserved flank, plus strand); MAT1-1-1 (core MAT gene, minus strand); MAT1-2-1 (core MAT gene, plus strand); APN2 (conserved flank, minus strand); COX13 (conserved flank, plus strand).65 kb70 kb75 kb80 kb31.6 kb more to contig end →called locusSLA2: conserved flank, 63,880–71,387 (+), identity 96.4%, search hit onlySLA2MAT1-1-1: core MAT gene, 73,880–75,049 (-), identity 81.5%, search hit onlyMAT1-1-1MAT1-2-1: core MAT gene, 75,896–76,209 (+), identity 74.5%, search hit onlyMAT1-2-1APN2: conserved flank, 77,129–79,460 (-), identity 93.2%, search hit onlyAPN2COX13: conserved flank, 79,700–80,442 (+), identity 93.4%, search hit onlyCOX13
Gene order on NKHU02000077. Scroll sideways to see the whole figure.
FungiDB release 71 gene models on NKHU02000077, 63,051 to 81,270CDV56_106667 63,880-71,387 (+): ANTH domain | I/LWEQ domain | Pleckstrin homology domain | domain-containing proteinCDV56_106667CDV56_107167 73,880-75,049 (-): Mating-type protein MAT alpha 1 HMG-box | domain-containing proteinCDV56_107167CDV56_107267 75,896-76,209 (+): unspecified productCDV56_107267CDV56_107330 77,129-79,460 (-): DNA-(apurinic or apyrimidinic site) endonuclease 2CDV56_107330CDV56_107450 79,700-80,442 (+): Cytochrome c oxidase subunit VIa | domain-containing proteinCDV56_107450CDV56_107499 80,870-83,497 (-): Anaphase-promoting complex subunit 5 | domain-containing proteinCDV56_107499
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
NKHU02000077:63,880–80,442 · 16.6 kb
Own genes
NKHU02000077:63,880–80,442 · 16.6 kb
Locus
Genes of both idiomorphs at one locus.
Genes modelled
5 of 5 gene hits
Nearest contig end
32.4 kb
Region (samtools)
NKHU02000077:63880-80442
Idiomorph scores
  • MAT1-1 590.0
  • MAT1-2 82.4

Margin over the next idiomorph: 507.6

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, proteome96.4cov 88.7%< 1e-1801,719 bits63,880–71,387 +–746128_a1163_MAT_MAT1-1CDV56_106667
MAT1-1-1core MAThit onlyDIAMOND, proteome81.5cov 100.0%1.7e-216590 bits73,880–75,049 -–746128_a1163_MAT_MAT1-1CDV56_107167
MAT1-2-1core MAThit onlyDIAMOND, proteome74.5cov 15.8%4.1e-2382 bits75,896–76,209 +–746128_af293_MAT_MAT1-2CDV56_107267
APN2conserved flankhit onlyDIAMOND, proteome93.2cov 36.7%< 1e-1801,044 bits77,129–79,460 -–2903220_liq80xsp_MAT_combinedCDV56_107330
COX13conserved flankhit onlyDIAMOND, proteome93.4cov 100.0%1.6e-87244 bits79,700–80,442 +–746128_af293_MAT_MAT1-2CDV56_107450

MAT1-2 MAT family · Ascomycota

medium confidence
Gene order of the MAT1-2 locus on NKHU02000492MAT1-2 locus: genes from left to right on NKHU02000492, 436 to 6,157: SLA2 (conserved flank, plus strand); MAT1-2-4 (core MAT gene, minus strand); CIMG_00407 (core MAT gene, minus strand); MAT1-1-3 (core MAT gene, plus strand); MAT1-2-1 (core MAT gene, plus strand).1 kb2 kb3 kb4 kb5 kb6 kbcontig endcalled locusSLA2: conserved flank, 436–1,151 (+), identity 80.9%, search hit onlySLA2MAT1-2-4: core MAT gene, 3,174–4,565 (-), identity 88.3%, search hit onlyMAT1-2-4CIMG_00407: core MAT gene, 3,748–3,972 (-), identity 26.667%, search hit onlyCIMG_00407MAT1-1-3: core MAT gene, 5,081–6,157 (+), identity 37.8%, search hit onlyMAT1-1-3 (lost to MAT1-2-1)MAT1-2-1: core MAT gene, 5,081–6,157 (+), identity 82.3%, search hit onlyMAT1-2-1
Gene order on NKHU02000492. Scroll sideways to see the whole figure.
FungiDB release 71 gene models on NKHU02000492, 1 to 6,457CDV56_100138 436-1,151 (+): I/LWEQ domain | domain-containing proteinCDV56_100138CDV56_100671 3,174-4,565 (-): putative mating locus proteinCDV56_100671 MAT1-2-4CDV56_100970 5,081-6,157 (+): HMG (high mobility group) box | domain-containing proteinCDV56_100970
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
  • MAT1-1-3 is a weak hit to the other idiomorph's gene and was not counted against the call.
Location
NKHU02000492:436–6,157 · 5.7 kb
Own genes
NKHU02000492:436–6,157 · 5.7 kb
Locus
Provisional: the call only tied the admission bar, or came from the relaxed pass.
Genes modelled
3 of 5 gene hits
Nearest contig end
435 bp
Region (samtools)
NKHU02000492:436-6157
Idiomorph scores
  • MAT1-2 533.0

Margin over the set-aside MAT1-1-3 hit: 44.5 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
MAT1-2-182.3MAT1-1-337.8100.0higher identity

Gene evidence

GeneRoleModel Identity %E-value Position (strand)Exons Reference recordFungiDB gene
SLA2conserved flankhit onlyDIAMOND, proteome80.9cov 20.0%7.9e-93284 bits436–1,151 +–746128_af293_MAT_MAT1-2CDV56_100138
MAT1-2-4core MAThit onlyDIAMOND, proteome88.3cov 99.2%2.4e-162447 bits3,174–4,565 -–746128_af293_MAT_MAT1-2CDV56_100671 MAT1-2-4
CIMG_00407core MAThit onlytblastn26.7cov 22.0%1.7e-0737 bits3,748–3,972 -–5501_rs_MAT_MAT1-2CDV56_100671 MAT1-2-4
MAT1-1-3core MATother idiomorph, not countedlost to MAT1-2-1, not countedhit onlyDIAMOND, proteome37.8cov 41.1%1.1e-1156 bits5,081–6,157 +–230073_uamh-1363_MAT_MAT1-1CDV56_100970
MAT1-2-1core MAThit onlyDIAMOND, proteome82.3cov 100.0%7.5e-196533 bits5,081–6,157 +–746128_af293_MAT_MAT1-2CDV56_100970
APN2expected, not found–
COX13expected, not found–

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
MATNKHU02000146:19,702–21,481MAT1-2MAT1-2-11too few of the family's genes found
MATNKHU02000420:1,256–3,443MAT1-2MAT1-2-11too few of the family's genes found
MATNKHU02000485:1,325–2,464undeterminedCOX131too few of the family's genes found

Provenance

Genome file
AthermomutatusHMRAF39.genome.fasta
Assembly
647 contigs · 30.9 Mb · N50 93.3 kb
Genome SHA-256
e8fb63deb48abfce7cb87b90c48f538c89d97d0c58f806d7f608855cb658e2c3
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': 1131492, 'routing_taxid_rank': 'family', 'flags': ['identical_to_reference'], '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
2026-11-07T02:36:25Z
Run time
69 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