MATPredict · mating-type report

CimmitisH538-4

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 02:30 UTC by MATPredict 0.8.1

Result

Mating type

MAT1-1high confidence

Called loci 1

MAT1-1 MAT family · Ascomycota

high confidence
Gene order of the MAT1-1 locus on DS016985MAT1-1 locus: genes from left to right on DS016985, 378,608 to 391,450: COX13 (conserved flank, minus strand); APN2 (conserved flank, plus strand); MAT1-1-4 (core MAT gene, plus strand); MAT1-1-1 (core MAT gene, plus strand); SLA2 (conserved flank, minus strand).380 kb385 kb390 kb← 378.0 kb more to contig endcalled locusCOX13: conserved flank, 378,608–379,303 (-), identity 100.0%, search hit onlyCOX13APN2: conserved flank, 379,931–381,756 (+), identity 100.0%, search hit onlyAPN2MAT1-1-4: core MAT gene, 382,539–383,743 (+), identity 99.4%, search hit onlyMAT1-1-4MAT1-1-1: core MAT gene, 384,173–385,395 (+), identity 98.5%, search hit onlyMAT1-1-1SLA2: conserved flank, 387,518–391,450 (-), identity 100.0%, search hit onlySLA2
Gene order on DS016985. Scroll sideways to see the whole figure.
FungiDB release 71 gene models on DS016985, 377,965 to 392,093CIHG_02235 378,608-379,303 (-): Cytochrome c oxidase subunit VIa | domain-containing proteinCIHG_02235CIHG_02236 379,931-381,756 (+): DNA-(apurinic or apyrimidinic site) lyase 2CIHG_02236CIHG_02237 382,539-383,743 (+): unspecified productCIHG_02237CIHG_02238 384,173-385,395 (+): mating-type protein MAT-1CIHG_02238CIHG_02239 385,896-386,343 (-): unspecified productCIHG_02239CIHG_02240 387,132-391,646 (-): huntingtin-interacting protein 1CIHG_02240CIHG_02241 392,022-394,765 (-): Maintenance of mitochondrial morphology protein 1 | Pleckstrin homology domain | domain-containing proteinCIHG_02241
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
Location
DS016985:378,608–391,450 · 12.8 kb
Own genes
DS016985:378,608–391,450 · 12.8 kb
Locus
Complete locus: MAT gene(s) with their flanking genes.
Genes modelled
5 of 5 gene hits
Nearest contig end
378.6 kb
Region (samtools)
DS016985:378608-391450
Idiomorph scores
  • MAT1-1 732.0

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
COX13conserved flankhit onlyDIAMOND, proteome100.0cov 100.0%3.4e-91254 bits378,608–379,303 -–199306_rmscc1040_MAT_MAT1-1CIHG_02235
APN2conserved flankhit onlyDIAMOND, proteome100.0cov 95.0%< 1e-1801,175 bits379,931–381,756 +–5501_h538-4_MAT_MAT1-1CIHG_02236
MAT1-1-4core MAThit onlyDIAMOND, proteome99.4cov 72.4%7.1e-128357 bits382,539–383,743 +–199306_rmscc1040_MAT_MAT1-1CIHG_02237
MAT1-1-1core MAThit onlyDIAMOND, proteome98.5cov 100.0%3.7e-272732 bits384,173–385,395 +–5501_h538-4_MAT_MAT1-1CIHG_02238
SLA2conserved flankhit onlyDIAMOND, proteome100.0cov 100.0%< 1e-1801,811 bits387,518–391,450 -–5501_rs_MAT_MAT1-2CIHG_02240

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
MATDS017008:111,135–113,247MAT1-2MAT1-2-11too few of the family's genes found

Provenance

Genome file
CimmitisH538-4.genome.fasta
Assembly
556 contigs · 27.8 Mb · N50 369.3 kb
Genome SHA-256
e0fb0c8609bddb7d0711ae122b60a6f2cffb73458e7484ba0cf2a87c6f8c3003
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': 33184, 'routing_taxid_rank': 'family', 'flags': ['high_N'], '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 33184', 'routed_by': 'family taxid 33184 (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
2026-11-07T02:30:02Z
Run time
47 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