MATPredict · mating-type report

AlentulusIFM54703

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 02:36 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 BCLY01000004MAT1-2 locus: genes from left to right on BCLY01000004, 2,550,877 to 2,563,998: 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).2,555 kb2,560 kb1,892.5 kb more to contig end →called locusCOX13: conserved flank, 2,550,877–2,551,618 (-), identity 95.6%, search hit onlyCOX13APN2: conserved flank, 2,551,978–2,554,165 (+), identity 93.2%, search hit onlyAPN2MAT1-1-3: core MAT gene, 2,555,080–2,556,156 (-), identity 34.0%, search hit onlyMAT1-1-3 (lost to MAT1-2-1)MAT1-2-1: core MAT gene, 2,555,080–2,556,156 (-), identity 89.4%, search hit onlyMAT1-2-1MAT1-2-4: core MAT gene, 2,556,672–2,557,507 (+), identity 95.53%, gene modelMAT1-2-4CIMG_00407: core MAT gene, 2,557,264–2,557,431 (+), identity 30.357%, search hit onlyCIMG_00407SLA2: conserved flank, 2,560,094–2,563,998 (-), identity 98.1%, search hit onlySLA2
Gene order on BCLY01000004. Scroll sideways to see the whole figure.
FungiDB release 71 gene models on BCLY01000004, 2,550,222 to 2,564,654TMP_alenIFM54703_2169 2,547,877-2,550,497 (+): Anaphase-promoting complex subunit 5 | domain-containing proteinTMP_alenIFM54703_2169TMP_alenIFM54703_2170 2,550,877-2,551,618 (-): cytochrome c oxidase subunit 6A, mitochondrialTMP_alenIFM54703_2170TMP_alenIFM54703_2171 2,551,978-2,554,165 (+): DNA-(apurinic or apyrimidinic site) lyase 2TMP_alenIFM54703_2171TMP_alenIFM54703_2172 2,555,080-2,556,156 (-): HMG (high mobility group) box | domain-containing proteinTMP_alenIFM54703_2172TMP_alenIFM54703_2173 2,560,094-2,563,998 (-): endocytosis protein end4TMP_alenIFM54703_2173
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
  • gene model
  • search hit only
  • MAT1-1-3 is a weak hit to the other idiomorph's gene and was not counted against the call.
Location
BCLY01000004:2,550,877–2,563,998 · 13.1 kb
Own genes
BCLY01000004:2,550,877–2,563,998 · 13.1 kb
Locus
Complete locus: MAT gene(s) with their flanking genes.
Genes modelled
5 of 7 gene hits
Nearest contig end
1.9 Mb
Region (samtools)
BCLY01000004:2550877-2563998
Idiomorph scores
  • MAT1-2 570.0

Margin over the set-aside MAT1-1-3 hit: 55.4 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
MAT1-2-189.4MAT1-1-334.0100.0higher identity

Gene evidence

GeneRoleModel Identity %E-value Position (strand)Exons Reference recordFungiDB gene
COX13conserved flankhit onlyDIAMOND, proteome95.6cov 100.0%1.2e-91254 bits2,550,877–2,551,618 -–746128_af293_MAT_MAT1-2TMP_alenIFM54703_2170
APN2conserved flankhit onlyDIAMOND, proteome93.2cov 36.7%< 1e-1801,155 bits2,551,978–2,554,165 +–2903220_liq80xsp_MAT_combinedTMP_alenIFM54703_2171
MAT1-1-3core MATother idiomorph, not countedlost to MAT1-2-1, not countedhit onlyDIAMOND, proteome34.0cov 52.2%2.7e-1154 bits2,555,080–2,556,156 -–230073_uamh-1363_MAT_MAT1-1TMP_alenIFM54703_2172
MAT1-2-1core MAThit onlyDIAMOND, proteome89.4cov 100.0%1.8e-210570 bits2,555,080–2,556,156 -–746128_af293_MAT_MAT1-2TMP_alenIFM54703_2172
MAT1-2-4core MATgene modelexonerate95.5cov 99.2%1.2e-101323 bits2,556,672–2,557,507 +3746128_af293_MAT_MAT1-2none
CIMG_00407core MAThit onlytblastn30.4cov 21.0%9.3e-0838 bits2,557,264–2,557,431 +–5501_rs_MAT_MAT1-2none
SLA2conserved flankhit onlyDIAMOND, proteome98.1cov 88.7%< 1e-1801,745 bits2,560,094–2,563,998 -–746128_a1163_MAT_MAT1-1TMP_alenIFM54703_2173

Withheld candidate loci 2

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 (2).

Show the 2 withheld loci

Withheld loci (2)

familylocationidiomorph genesmodelledreason
MATBCLY01000009:2,216,652–2,218,824MAT1-2MAT1-2-11too few of the family's genes found
MATBCLY01000009:2,650,620–2,650,868MAT1-1MAT1-1-1, MAT1-1-31too few of the family's genes found

Provenance

Genome file
AlentulusIFM54703.genome.fasta
Assembly
12 contigs · 30.8 Mb · N50 4.2 Mb
Genome SHA-256
d78db52ff00571ddd262727c0459c3a845c98b751742c25868a79c121a70acc2
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
2026-11-07T02:35:19Z
Run time
53 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