MATPredict · mating-type report

ClusitaniaeATCC42720

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 01:53 UTC by MATPredict 0.8.1

Result

Mating type

alphahigh confidence

Called loci 1

alpha MTL family · Ascomycota

high confidence
Gene order of the alpha locus on CH408081alpha locus: genes from left to right on CH408081, 200,484 to 207,399: PAP1 (variable flank, plus strand); MTLalpha1 (core MAT gene, minus strand); PIK1 (variable flank, minus strand); OBP1 (variable flank, minus strand).202 kb204 kb206 kb← 200.1 kb more to contig endcalled locusPAP1: variable flank, 200,484–202,157 (+), identity 76.6%, search hit onlyPAP1MTLalpha1: core MAT gene, 202,174–202,641 (-), identity 38.7%, search hit onlyMTLalpha1PIK1: variable flank, 202,826–205,609 (-), identity 66.0%, search hit onlyPIK1OBP1: variable flank, 206,185–207,399 (-), identity 68.0%, search hit onlyOBP1
Gene order on CH408081. Scroll sideways to see the whole figure.
FungiDB release 68 gene models on CH408081, 200,139 to 207,744CLUG_04920 197,828-200,389 (+): hypothetical proteinCLUG_04920CLUG_04922 200,484-202,157 (+): hypothetical proteinCLUG_04922CLUG_04923 202,174-202,641 (-): hypothetical proteinCLUG_04923CLUG_04924 202,826-205,609 (-): hypothetical proteinCLUG_04924CLUG_04925 206,185-207,399 (-): hypothetical proteinCLUG_04925
FungiDB release 68 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
  • variable flank
  • search hit only
Location
CH408081:200,484–207,399 · 6.9 kb
Cross-lineage class
MAT1-1
Own genes
CH408081:200,484–207,399 · 6.9 kb
Locus
Complete locus: MAT gene(s) with their flanking genes.
Genes modelled
4 of 4 gene hits
Nearest contig end
200.5 kb
Region (samtools)
CH408081:200484-207399
Idiomorph scores
  • alpha 84.7

No other idiomorph scored.

Score: bitscore of the best core-gene hit for each idiomorph.

Gene evidence

GeneRoleModel Identity %E-value Position (strand)Exons Reference recordFungiDB gene
PAP1variable flankhit onlyDIAMOND, proteome76.6cov 99.5%1.8e-322873 bits200,484–202,157 +–498019_b11221_MTL_alphaCLUG_04922
MTLalpha1core MAThit onlyDIAMOND, proteome38.7cov 58.0%9.0e-2485 bits202,174–202,641 -–4959_cbs767_MTL_ACLUG_04923
PIK1variable flankhit onlyDIAMOND, proteome66.0cov 100.0%< 1e-1801,126 bits202,826–205,609 -–498019_b11221_MTL_alphaCLUG_04924
OBP1variable flankhit onlyDIAMOND, proteome68.0cov 99.5%5.9e-197542 bits206,185–207,399 -–498019_b11221_MTL_alphaCLUG_04925

Withheld candidate loci 41

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: fewer than 2 genes could be modelled (37); too few of the family's genes found (4).

Show the 41 withheld loci

Withheld loci (41)

familylocationidiomorph genesmodelledreason
MTLCH408076:34,822–34,920AMTLA20fewer than 2 genes could be modelled
MTLCH408076:300,139–300,339AMTLA10fewer than 2 genes could be modelled
MTLCH408076:514,110–514,403alphaMTLalpha10fewer than 2 genes could be modelled
MTLCH408076:1,006,788–1,006,877AMTLA20fewer than 2 genes could be modelled
MTLCH408076:1,145,922–1,146,143alphaMTLalpha10fewer than 2 genes could be modelled
MTLCH408076:1,281,726–1,281,827alphaMTLalpha10fewer than 2 genes could be modelled
MTLCH408076:1,415,822–1,416,010AMTLA10fewer than 2 genes could be modelled
MTLCH408076:1,842,814–1,843,086AMTLA10fewer than 2 genes could be modelled
MTLCH408076:2,038,840–2,038,953AMTLA10fewer than 2 genes could be modelled
MTLCH408076:2,223,777–2,223,902alphaMTLalpha10fewer than 2 genes could be modelled
MTLCH408076:2,254,427–2,254,666AMTLA20fewer than 2 genes could be modelled
MTLCH408077:804,872–824,019alphaMTLalpha10fewer than 2 genes could be modelled
MTLCH408077:1,016,905–1,016,994alphaMTLalpha10fewer than 2 genes could be modelled
MTLCH408077:1,153,109–1,153,354AMTLA20fewer than 2 genes could be modelled
MTLCH408077:1,224,101–1,224,280AMTLA10fewer than 2 genes could be modelled
MTLCH408077:1,775,435–1,790,895AMTLA20fewer than 2 genes could be modelled
MTLCH408077:2,086,282–2,086,377alphaMTLalpha10fewer than 2 genes could be modelled
MTLCH408077:2,169,854–2,194,424AMTLA1, MTLalpha10fewer than 2 genes could be modelled
MTLCH408078:505,531–505,791AMTLA20fewer than 2 genes could be modelled
MTLCH408078:789,029–803,232AMTLA1, MTLA20fewer than 2 genes could be modelled
MTLCH408081:547,145–547,258AMTLA20fewer than 2 genes could be modelled
MTLCH408080:175,914–176,102AMTLA20fewer than 2 genes could be modelled
MTLCH408080:320,892–343,900AMTLA1, MTLalpha10fewer than 2 genes could be modelled
MTLCH408080:717,903–718,136AMTLA20fewer than 2 genes could be modelled
MTLCH408080:1,324,557–1,324,655alphaMTLalpha10fewer than 2 genes could be modelled
MTLCH408079:179,366–179,470alphaMTLalpha10fewer than 2 genes could be modelled
MTLCH408079:238,646–238,813alphaMTLalpha10fewer than 2 genes could be modelled
MTLCH408079:375,176–375,322AMTLA10fewer than 2 genes could be modelled
MTLCH408079:406,179–406,268alphaMTLalpha10fewer than 2 genes could be modelled
MTLCH408079:486,772–486,915alphaMTLalpha10fewer than 2 genes could be modelled
MTLCH408079:692,416–692,547AMTLA10fewer than 2 genes could be modelled
MTLCH408079:1,195,091–1,195,378alphaMTLalpha10fewer than 2 genes could be modelled
MTLCH408079:1,279,786–1,279,914AMTLA20fewer than 2 genes could be modelled
MTLCH408082:250,861–250,980alphaMTLalpha10fewer than 2 genes could be modelled
MTLCH408082:348,441–348,749AMTLA10fewer than 2 genes could be modelled
MTLCH408083:174,409–174,519alphaMTLalpha10fewer than 2 genes could be modelled
MTLCH408083:629,735–637,284AMTLA1, MTLA20fewer than 2 genes could be modelled
MTLCH408076:1,637,699–1,640,230undeterminedOBP11too few of the family's genes found
MTLCH408077:590,055–592,370undeterminedPIK11too few of the family's genes found
MTLCH408078:124,259–125,968undeterminedOBP11too few of the family's genes found
MTLCH408078:1,455,710–1,458,778undeterminedPIK11too few of the family's genes found

Provenance

Genome file
ClusitaniaeATCC42720.genome.fasta
Assembly
9 contigs · 12.1 Mb · N50 1.9 Mb
Genome SHA-256
3d2257fb7a3dc5b295420c0757663806c9bb68d8c1b1c923138be1a332629892
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': 27319, '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': 12, 'genetic_code_from': 'family taxid 27319', 'routed_by': 'family taxid 27319 (lineage)'}, genetic_code=12, 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, supported_min_bitscore=33.0
Run started
2026-11-07T01:53:29Z
Run time
22 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