MATPredict · mating-type report

AfumigatusAf293

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 02:31 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 Chr3_A_fumigatus_Af293MAT1-2 locus: genes from left to right on Chr3_A_fumigatus_Af293, 1,516,711 to 1,529,806: 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); APN2 (conserved flank, minus strand); COX13 (conserved flank, plus strand).1,520 kb1,525 kb1,530 kb← 1,516.1 kb more to contig endcalled locusSLA2: conserved flank, 1,516,711–1,520,611 (+), identity 100.0%, search hit onlySLA2MAT1-2-4: core MAT gene, 1,523,105–1,524,006 (-), identity 100.0%, search hit onlyMAT1-2-4CIMG_00407: core MAT gene, 1,523,248–1,523,790 (-), identity 23.077%, search hit onlyCIMG_00407MAT1-1-3: core MAT gene, 1,524,532–1,525,609 (+), identity 32.0%, search hit onlyMAT1-1-3 (lost to MAT1-2-1)MAT1-2-1: core MAT gene, 1,524,532–1,525,609 (+), identity 100.0%, search hit onlyMAT1-2-1APN2: conserved flank, 1,526,518–1,528,706 (-), identity 100.0%, search hit onlyAPN2COX13: conserved flank, 1,529,066–1,529,806 (+), identity 100.0%, search hit onlyCOX13
Gene order on Chr3_A_fumigatus_Af293. Scroll sideways to see the whole figure.
FungiDB release 71 gene models on Chr3_A_fumigatus_Af293, 1,516,056 to 1,530,460Afu3g06130 1,512,526-1,516,290 (+): Ortholog(s) have lipid binding activity and endoplasmic reticulum, nucleus-vacuole junction, plasma membrane, ribosome localizationAfu3g06130Afu3g06140 1,516,449-1,520,994 (+): Ortholog(s) have role in actin filament organization, activation of bipolar cell growth, cellular protein localization, cortical actin cytoskeleton organization, endocytosis and establishment of cell polarity, moreAfu3g06140Afu3g06160 1,523,105-1,524,006 (-): MAT1-2-4Afu3g06160 MAT1-2-4Afu3g06170 1,524,532-1,525,609 (+): HMG box mating-type transcription factorAfu3g06170 MAT1-2Afu3g06180 1,526,148-1,528,852 (-): Ortholog(s) have DNA-(apurinic or apyrimidinic site) lyase activity, double-stranded DNA 3'-5' exodeoxyribonuclease activity, phosphodiesterase I activityAfu3g06180Afu3g06190 1,528,982-1,530,023 (+): Cytochrome c oxidase subunit ViaAfu3g06190Afu3g06200 1,530,206-1,532,828 (-): Ortholog(s) have anaphase-promoting complex localizationAfu3g06200
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
Chr3_A_fumigatus_Af293:1,516,711–1,529,806 · 13.1 kb
Own genes
Chr3_A_fumigatus_Af293:1,516,711–1,529,806 · 13.1 kb
Locus
Complete locus: MAT gene(s) with their flanking genes.
Genes modelled
5 of 7 gene hits
Nearest contig end
1.5 Mb
Region (samtools)
Chr3_A_fumigatus_Af293:1516711-1529806
Idiomorph scores
  • MAT1-2 630.0

Margin over the set-aside MAT1-1-3 hit: 68.0 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
MAT1-2-1100.0MAT1-1-332.0100.0higher identity

Gene evidence

GeneRoleModel Identity %E-value Position (strand)Exons Reference recordFungiDB gene
SLA2conserved flankhit onlyDIAMOND, proteome100.0cov 100.0%< 1e-1801,764 bits1,516,711–1,520,611 +–746128_af293_MAT_MAT1-2Afu3g06140
MAT1-2-4core MAThit onlyDIAMOND, proteome100.0cov 100.0%3.3e-186503 bits1,523,105–1,524,006 -–746128_af293_MAT_MAT1-2Afu3g06160 MAT1-2-4
CIMG_00407core MAThit onlytblastn23.1cov 62.0%6.8e-1059 bits1,523,248–1,523,790 -–5501_rs_MAT_MAT1-2Afu3g06160 MAT1-2-4
MAT1-1-3core MATother idiomorph, not countedlost to MAT1-2-1, not countedhit onlyDIAMOND, proteome32.0cov 52.2%8.0e-1256 bits1,524,532–1,525,609 +–230073_uamh-1363_MAT_MAT1-1Afu3g06170 MAT1-2
MAT1-2-1core MAThit onlyDIAMOND, proteome100.0cov 100.0%6.0e-234630 bits1,524,532–1,525,609 +–746128_af293_MAT_MAT1-2Afu3g06170 MAT1-2
APN2conserved flankhit onlyDIAMOND, proteome100.0cov 100.0%< 1e-1801,295 bits1,526,518–1,528,706 -–746128_a1163_MAT_MAT1-1Afu3g06180
COX13conserved flankhit onlyDIAMOND, proteome100.0cov 100.0%1.5e-92257 bits1,529,066–1,529,806 +–746128_af293_MAT_MAT1-2Afu3g06190

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
MATChr4_A_fumigatus_Af293:2,829,001–2,831,175MAT1-2MAT1-2-11too few of the family's genes found

Provenance

Genome file
AfumigatusAf293.genome.fasta
Assembly
9 contigs · 29.4 Mb · N50 3.9 Mb
Genome SHA-256
971529acb7fb0822140135d7d8e2eca06c1eba4f740340c7f56f0263c2081d2f
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
2026-11-07T02:30:32Z
Run time
48 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