MATPredict · mating-type report

PlingamJN3

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 02:52 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 FP929126MAT1-2 locus: genes from left to right on FP929126, 554,610 to 582,082: MAT1-2-1 (core MAT gene, plus strand); MAT1-1-3 (core MAT gene, plus strand); APN2 (conserved flank, minus strand); COX13 (conserved flank, plus strand); MAT1-1-4 (core MAT gene, plus strand).555 kb560 kb565 kb570 kb575 kb580 kb504.5 kb more to contig end →called locusMAT1-2-1: core MAT gene, 554,610–555,882 (+), identity 98.5%, search hit onlyMAT1-2-1MAT1-1-3: core MAT gene, 554,961–555,074 (+), identity 36.842%, search hit onlyMAT1-1-3 (lost to MAT1-2-1)APN2: conserved flank, 558,980–560,932 (-), identity 84.1%, search hit onlyAPN2COX13: conserved flank, 561,318–561,980 (+), identity 48.6%, search hit onlyCOX13MAT1-1-4: core MAT gene, 581,957–582,082 (+), identity 40.426%, search hit onlyMAT1-1-4
Gene order on FP929126. Scroll sideways to see the whole figure.
FungiDB release 71 gene models on FP929126, 553,238 to 583,456LEMA_P114380.1 552,415-553,355 (+): similar to pyridoxamine phosphate oxidaseLEMA_P114380.1LEMA_P114390.1 554,610-555,882 (+): HMG (high mobility group) box | domain-containing proteinLEMA_P114390.1LEMA_P114400.1 557,805-558,191 (+): unspecified productLEMA_P114400.1LEMA_P114410.1 558,371-558,532 (+): unspecified productLEMA_P114410.1LEMA_P114420.1 558,980-560,932 (-): similar to DNA lyaseLEMA_P114420.1LEMA_P114430.1 561,318-561,980 (+): similar to cytochrome c oxidase subunit VIaLEMA_P114430.1LEMA_P114440.1 562,197-565,010 (-): similar to anaphase-promoting complex subunit Apc5LEMA_P114440.1LEMA_P114450.1 565,196-566,077 (-): similar to complex I intermediate-associated protein CIA30LEMA_P114450.1LEMA_P114460.1 566,430-567,681 (+): similar to mitochondrial carrier protein rim2LEMA_P114460.1LEMA_P114470.1 568,199-569,525 (+): unspecified productLEMA_P114470.1LEMA_P114480.1 569,966-570,484 (-): Translation initiation factor SUI1 | domain-containing proteinLEMA_P114480.1LEMA_P114490.1 570,897-571,831 (-): PAT complex subunit Asterix | domain-containing proteinLEMA_P114490.1LEMA_P114500.1 572,596-577,678 (+): Transcription mediator complex subunit Med12 | SRB8 ARM-like domain | domain-containing proteinLEMA_P114500.1LEMA_P114510.1 578,156-579,147 (-): similar to phosphoribosylaminoimidazole-succinocarboxamide synthaseLEMA_P114510.1LEMA_P114520.1 579,552-582,772 (+): Autophagy-related protein 29LEMA_P114520.1LEMA_P114530.1 583,044-583,986 (-): SUR7/PalI family | domain-containing proteinLEMA_P114530.1
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.
  • MAT1-1-4 is a weak hit to the other idiomorph's gene and was not counted against the call.
Location
FP929126:554,610–582,082 · 27.5 kb
Own genes
FP929126:554,610–582,082 · 27.5 kb
Locus
Complete locus: MAT gene(s) with their flanking genes.
Genes modelled
3 of 5 gene hits
Nearest contig end
505.9 kb
Region (samtools)
FP929126:554610-582082
Idiomorph scores
  • MAT1-2 711.0
  • MAT1-1 33.5

Margin over the next idiomorph: 677.5

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
MAT1-2-198.5MAT1-1-336.8100.0higher identity

Gene evidence

GeneRoleModel Identity %E-value Position (strand)Exons Reference recordFungiDB gene
MAT1-2-1core MAThit onlyDIAMOND, proteome98.5cov 100.0%2.1e-263711 bits554,610–555,882 +–5022_unknown-2_MAT_MAT1-2LEMA_P114390.1
MAT1-1-3core MATother idiomorph, not countedlost to MAT1-2-1, not countedhit onlytblastn36.8cov 21.0%6.7e-0437 bits554,961–555,074 +–230073_uamh-1363_MAT_MAT1-1LEMA_P114390.1
APN2conserved flankhit onlyDIAMOND, proteome84.1cov 36.7%8.6e-212600 bits558,980–560,932 -–2903220_liq80xsp_MAT_combinedLEMA_P114420.1
COX13conserved flankhit onlyDIAMOND, proteome48.6cov 97.7%3.9e-36114 bits561,318–561,980 +–578113_sxlc146_MAT_MAT1-2LEMA_P114430.1
MAT1-1-4core MATother idiomorph, not countedhit onlytblastn40.4cov 15.0%1.8e-0134 bits581,957–582,082 +–199306_rmscc1040_MAT_MAT1-1LEMA_P114520.1
MAT1-1-1expected, not found–
SLA2expected, 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 (2); fewer than 2 genes could be modelled (1).

Show the 3 withheld loci

Withheld loci (3)

familylocationidiomorph genesmodelledreason
MATFP929123:456,335–479,726MAT1-1MAT1-1-1, SLA21fewer than 2 genes could be modelled
MATFP929105:1,220,263–1,222,472MAT1-2MAT1-2-11too few of the family's genes found
MATFP929094:1,100,938–1,115,954MAT1-2MAT1-1-1, MAT1-2-11too few of the family's genes found

Provenance

Genome file
PlingamJN3.genome.fasta
Assembly
76 contigs · 45.1 Mb · N50 1.8 Mb
Genome SHA-256
b819485a8ffc0c3e11a20bc41a44530d430eb16ff52f34670fdb3c7322c054d4
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': 34374, '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 34374', 'routed_by': 'family taxid 34374 (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
2026-11-07T02:50:54Z
Run time
96 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