MATPredict · mating-type report

AfijiensisCBS313.89

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 02:24 UTC by MATPredict 0.8.1

Result

Mating type

MAT1-2high confidence

Called loci 1

MAT1-2 MAT family · Ascomycota

high confidence
Gene order of the MAT1-2 locus on KZ824647MAT1-2 locus: genes from left to right on KZ824647, 277,896 to 322,503: MAT1-1-2 (core MAT gene, plus strand); COX13 (conserved flank, minus strand); APN2 (conserved flank, plus strand); MAT1-1-3 (core MAT gene, minus strand); MAT1-2-1 (core MAT gene, minus strand); MAT1-2-4 (core MAT gene, plus strand); CIMG_00407 (core MAT gene, plus strand); SLA2 (conserved flank, minus strand).280 kb290 kb300 kb310 kb320 kb101.5 kb more to contig end →called locusMAT1-1-2: core MAT gene, 277,896–278,168 (+), identity 29.293%, search hit onlyMAT1-1-2COX13: conserved flank, 298,918–299,780 (-), identity 78.1%, search hit onlyCOX13APN2: conserved flank, 300,193–302,351 (+), identity 90.9%, search hit onlyAPN2MAT1-1-3: core MAT gene, 303,617–304,682 (-), identity 37.8%, search hit onlyMAT1-1-3 (lost to MAT1-2-1)MAT1-2-1: core MAT gene, 303,617–304,682 (-), identity 63.5%, search hit onlyMAT1-2-1MAT1-2-4: core MAT gene, 305,232–306,059 (+), identity 41.0%, search hit onlyMAT1-2-4CIMG_00407: core MAT gene, 305,457–305,717 (+), identity 28.571%, search hit onlyCIMG_00407SLA2: conserved flank, 318,641–322,503 (-), identity 89.6%, search hit onlySLA2
Gene order on KZ824647. Scroll sideways to see the whole figure.
FungiDB release 71 gene models on KZ824647, 275,669 to 324,733BO72DRAFT_127028 278,054-283,426 (+): mediator of RNA polymerase II transcription subunit 12BO72DRAFT_127028BO72DRAFT_486573 283,745-285,319 (+): CIA30-domain-containing proteinBO72DRAFT_486573BO72DRAFT_448691 285,386-286,687 (-): SAICAR synthetaseBO72DRAFT_448691BO72DRAFT_448693 286,840-288,904 (-): D-xylose reductase [NAD(P)H]BO72DRAFT_448693BO72DRAFT_448694 291,211-292,016 (-): unspecified productBO72DRAFT_448694BO72DRAFT_430417 292,798-294,657 (+): alpha/beta-hydrolaseBO72DRAFT_430417BO72DRAFT_448695 295,315-298,562 (+): putative anaphase-promoting complex subunit Apc5BO72DRAFT_448695BO72DRAFT_405513 298,860-299,780 (-): mitochondrial cytochrome c oxidase subunit VIaBO72DRAFT_405513BO72DRAFT_486580 300,093-302,351 (+): DNA lyase Apn2BO72DRAFT_486580BO72DRAFT_405520 303,118-304,682 (-): mating-type HMG-box protein MAT1-2BO72DRAFT_405520BO72DRAFT_405521 305,130-306,059 (+): putative mating locus proteinBO72DRAFT_405521BO72DRAFT_448699 309,496-311,124 (+): metal dependent phosphohydrolaseBO72DRAFT_448699BO72DRAFT_448700 311,055-312,844 (-): putative aldehyde dehydrogenase family proteinBO72DRAFT_448700BO72DRAFT_127623 312,965-315,129 (+): CAIB/BAIF family enzymeBO72DRAFT_127623BO72DRAFT_469111 315,343-318,008 (+): FAD/NAD(P)-binding domain-containing proteinBO72DRAFT_469111BO72DRAFT_486585 318,313-322,846 (-): cytoskeleton assembly control protein Sla2BO72DRAFT_486585BO72DRAFT_127709 323,236-326,440 (-): Pleckstrin homology domain | Maintenance of mitochondrial morphology protein 1 | domain-containing proteinBO72DRAFT_127709
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
  • MAT1-1-2 is a weak hit to the other idiomorph's gene and was not counted against the call.
  • MAT1-1-3 is a weak hit to the other idiomorph's gene and was not counted against the call.
Location
KZ824647:277,896–322,503 · 44.6 kb
Own genes
KZ824647:277,896–322,503 · 44.6 kb
Locus
Complete locus: MAT gene(s) with their flanking genes.
Genes modelled
5 of 8 gene hits
Nearest contig end
103.7 kb
Region (samtools)
KZ824647:277896-322503
Idiomorph scores
  • MAT1-2 263.0
  • MAT1-1 30.8

Margin over the next idiomorph: 232.2

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
MAT1-2-163.5MAT1-1-337.8100.0higher identity

Gene evidence

GeneRoleModel Identity %E-value Position (strand)Exons Reference recordFungiDB gene
MAT1-1-2core MATother idiomorph, not countedhit onlytblastn29.3cov 25.0%1.8e+0031 bits277,896–278,168 +–5141_74-ors-a_MAT_MAT1-1BO72DRAFT_127028
COX13conserved flankhit onlyDIAMOND, proteome78.1cov 100.0%8.9e-74209 bits298,918–299,780 -–746128_af293_MAT_MAT1-2BO72DRAFT_405513
APN2conserved flankhit onlyDIAMOND, proteome90.9cov 36.7%5.7e-309846 bits300,193–302,351 +–2903220_liq80xsp_MAT_combinedBO72DRAFT_486580
MAT1-1-3core MATother idiomorph, not countedlost to MAT1-2-1, not countedhit onlyDIAMOND, proteome37.8cov 41.1%1.2e-1258 bits303,617–304,682 -–230073_uamh-1363_MAT_MAT1-1BO72DRAFT_405520
MAT1-2-1core MAThit onlyDIAMOND, proteome63.5cov 24.2%1.8e-89263 bits303,617–304,682 -–1301501_voucher-267_MAT_MAT1-2BO72DRAFT_405520
MAT1-2-4core MAThit onlyDIAMOND, proteome41.0cov 97.6%5.6e-62188 bits305,232–306,059 +–746128_af293_MAT_MAT1-2BO72DRAFT_405521
CIMG_00407core MAThit onlytblastn28.6cov 33.0%2.8e-0236 bits305,457–305,717 +–5501_rs_MAT_MAT1-2BO72DRAFT_405521
SLA2conserved flankhit onlyDIAMOND, proteome89.6cov 100.0%< 1e-1801,612 bits318,641–322,503 -–746128_af293_MAT_MAT1-2BO72DRAFT_486585
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
MATKZ824621:638,402–645,236MAT1-2MAT1-2-1, MAT1-2-101too few of the family's genes found

Provenance

Genome file
AfijiensisCBS313.89.genome.fasta
Assembly
149 contigs · 36.5 Mb · N50 411.5 kb
Genome SHA-256
b6cd225c57555962d37dc12533a14e6e55f6e6ff11366ef871c4be3baec3d5c9
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': 1131492, '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 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
2026-11-07T02:22:54Z
Run time
77 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