MATPredict · mating-type report

AluchuensisIFO4308

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 02:12 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 DF126454MAT1-2 locus: genes from left to right on DF126454, 264,372 to 285,492: 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).265 kb270 kb275 kb280 kb285 kb← 263.3 kb more to contig endcalled locusSLA2: conserved flank, 264,372–268,185 (+), identity 89.5%, search hit onlySLA2MAT1-2-4: core MAT gene, 278,919–279,413 (-), identity 43.3%, search hit onlyMAT1-2-4CIMG_00407: core MAT gene, 278,922–279,194 (-), identity 23.913%, search hit onlyCIMG_00407MAT1-1-3: core MAT gene, 279,898–281,005 (+), identity 35.1%, search hit onlyMAT1-1-3 (lost to MAT1-2-1)MAT1-2-1: core MAT gene, 279,898–281,005 (+), identity 57.0%, search hit onlyMAT1-2-1APN2: conserved flank, 282,082–284,219 (-), identity 90.9%, search hit onlyAPN2COX13: conserved flank, 284,776–285,492 (+), identity 78.7%, search hit onlyCOX13
Gene order on DF126454. Scroll sideways to see the whole figure.
FungiDB release 71 gene models on DF126454, 263,317 to 286,547AKAW_03825 260,528-263,420 (+): PH domain-containing proteinAKAW_03825AKAW_03826 264,372-268,185 (+): cytoskeleton assembly control protein Sla2AKAW_03826AKAW_03827 268,572-270,209 (-): salicylate hydroxylaseAKAW_03827AKAW_03828 270,669-272,132 (-): CAIB/BAIF family enzymeAKAW_03828AKAW_03829 272,693-274,192 (+): aldehyde dehydrogenase family proteinAKAW_03829AKAW_03830 274,509-275,888 (-): WD domain, G-beta repeat | domain-containing proteinAKAW_03830AKAW_03831 278,919-279,413 (-): hypothetical proteinAKAW_03831AKAW_03832 279,898-281,005 (+): mating-type HMG-box protein MAT1-2AKAW_03832AKAW_03833 282,082-284,219 (-): DNA lyase Apn2AKAW_03833AKAW_03834 284,776-285,492 (+): cytochrome c oxidase subunit VIaAKAW_03834
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
DF126454:264,372–285,492 · 21.1 kb
Own genes
DF126454:264,372–285,492 · 21.1 kb
Locus
Complete locus: MAT gene(s) with their flanking genes.
Genes modelled
5 of 7 gene hits
Nearest contig end
264.4 kb
Region (samtools)
DF126454:264372-285492
Idiomorph scores
  • MAT1-2 295.0

Margin over the set-aside MAT1-1-3 hit: 21.9 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
MAT1-2-157.0MAT1-1-335.1100.0higher identity

Gene evidence

GeneRoleModel Identity %E-value Position (strand)Exons Reference recordFungiDB gene
SLA2conserved flankhit onlyDIAMOND, proteome89.5cov 100.0%< 1e-1801,583 bits264,372–268,185 +–746128_af293_MAT_MAT1-2AKAW_03826
MAT1-2-4core MAThit onlyDIAMOND, proteome43.3cov 65.6%1.7e-40130 bits278,919–279,413 -–746128_af293_MAT_MAT1-2AKAW_03831
CIMG_00407core MAThit onlytblastn23.9cov 35.0%5.8e-0235 bits278,922–279,194 -–5501_rs_MAT_MAT1-2AKAW_03831
MAT1-1-3core MATother idiomorph, not countedlost to MAT1-2-1, not countedhit onlyDIAMOND, proteome35.1cov 41.1%7.3e-1359 bits279,898–281,005 +–230073_uamh-1363_MAT_MAT1-1AKAW_03832
MAT1-2-1core MAThit onlyDIAMOND, proteome57.0cov 26.5%1.3e-101295 bits279,898–281,005 +–1301501_voucher-267_MAT_MAT1-2AKAW_03832
APN2conserved flankhit onlyDIAMOND, proteome90.9cov 36.7%< 1e-180905 bits282,082–284,219 -–2903220_liq80xsp_MAT_combinedAKAW_03833
COX13conserved flankhit onlyDIAMOND, proteome78.7cov 100.0%1.8e-74211 bits284,776–285,492 +–746128_af293_MAT_MAT1-2AKAW_03834

Withheld candidate loci 7

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 (7).

Show the 7 withheld loci

Withheld loci (7)

familylocationidiomorph genesmodelledreason
MATDF126448:1,463,556–1,465,748MAT1-2MAT1-2-11too few of the family's genes found
MATDF126465:570,202–571,613MAT1-1MAT1-1-1, MAT1-1-31too few of the family's genes found
MATDF126465:598,592–616,150MAT1-2MAT1-1-1, MAT1-2-11too few of the family's genes found
MATDF126492:82,262–83,589MAT1-1MAT1-1-31too few of the family's genes found
MATDF126520:23,151–38,757MAT1-1MAT1-1-1, MAT1-1-31too few of the family's genes found
MATDF126555:3,962–8,813MAT1-2MAT1-2-11too few of the family's genes found
MATDF126569:3,975–4,526MAT1-2MAT1-2-11too few of the family's genes found

Provenance

Genome file
AluchuensisIFO4308.genome.fasta
Assembly
1,163 contigs · 37.1 Mb · N50 790.1 kb
Genome SHA-256
b12e426dc6a2ad2fe40c7fa2212b68a01f353ab1c5fdc1e727ee8e285aeb900f
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
2026-11-07T02:10:42Z
Run time
87 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