MATPredict · mating-type report

CmilitarisATCC34164

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 02:18 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 CP023324MAT1-2 locus: genes from left to right on CP023324, 6,355,673 to 6,372,067: SLA2 (conserved flank, plus 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).6,355 kb6,360 kb6,365 kb6,370 kb1,913.6 kb more to contig end →called locusSLA2: conserved flank, 6,355,673–6,359,244 (+), identity 80.9%, search hit onlySLA2MAT1-1-3: core MAT gene, 6,366,569–6,367,388 (+), identity 36.5%, search hit onlyMAT1-1-3 (lost to MAT1-2-1)MAT1-2-1: core MAT gene, 6,366,569–6,367,388 (+), identity 55.8%, search hit onlyMAT1-2-1APN2: conserved flank, 6,368,643–6,370,852 (-), identity 88.6%, search hit onlyAPN2COX13: conserved flank, 6,371,303–6,372,067 (+), identity 64.9%, search hit onlyCOX13
Gene order on CP023324. Scroll sideways to see the whole figure.
FungiDB release 71 gene models on CP023324, 6,354,854 to 6,372,886A9K55_008813 6,348,516-6,354,900 (+): ankyrin 2,3A9K55_008813A9K55_008814 6,355,673-6,359,244 (+): cytoskeleton assembly control Sla2A9K55_008814A9K55_008815 6,362,023-6,363,097 (+): unspecified productA9K55_008815A9K55_008816 6,363,148-6,364,005 (+): unspecified productA9K55_008816A9K55_008817 6,366,569-6,367,388 (+): mating-type MAT1-2-1A9K55_008817A9K55_008818 6,368,643-6,370,852 (-): DNA lyaseA9K55_008818A9K55_008819 6,371,303-6,372,067 (+): Cytochrome c subunit VIaA9K55_008819A9K55_008820 6,372,694-6,375,153 (+): anaphase-promoting complex subunitA9K55_008820
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
CP023324:6,355,673–6,372,067 · 16.4 kb
Own genes
CP023324:6,355,673–6,372,067 · 16.4 kb
Locus
Complete locus: MAT gene(s) with their flanking genes.
Genes modelled
4 of 5 gene hits
Nearest contig end
1.9 Mb
Region (samtools)
CP023324:6355673-6372067
Idiomorph scores
  • MAT1-2 117.0

Margin over the set-aside MAT1-1-3 hit: 19.3 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
MAT1-2-155.8MAT1-1-336.5100.0higher identity

Gene evidence

GeneRoleModel Identity %E-value Position (strand)Exons Reference recordFungiDB gene
SLA2conserved flankhit onlyDIAMOND, proteome80.9cov 100.0%< 1e-1801,447 bits6,355,673–6,359,244 +–107463_unknown-1_MAT_MAT1-2A9K55_008814
MAT1-1-3core MATother idiomorph, not countedlost to MAT1-2-1, not countedhit onlyDIAMOND, proteome36.5cov 41.1%9.1e-1152 bits6,366,569–6,367,388 +–230073_uamh-1363_MAT_MAT1-1A9K55_008817
MAT1-2-1core MAThit onlyDIAMOND, proteome55.8cov 61.1%9.9e-35117 bits6,366,569–6,367,388 +–61372_suf959_MAT_MAT1-2A9K55_008817
APN2conserved flankhit onlyDIAMOND, proteome88.6cov 36.7%1.6e-214605 bits6,368,643–6,370,852 -–2903220_liq80xsp_MAT_combinedA9K55_008818
COX13conserved flankhit onlyDIAMOND, proteome64.9cov 100.0%3.3e-59172 bits6,371,303–6,372,067 +–27337_vdls-17_MAT_MAT1-2A9K55_008819

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
MATCP023327:663,296–665,381MAT1-2MAT1-2-11too few of the family's genes found
MATCP023324:4,445,441–4,446,834MAT1-2MAT1-2-11too few of the family's genes found

Provenance

Genome file
CmilitarisATCC34164.genome.fasta
Assembly
7 contigs · 33.6 Mb · N50 5.8 Mb
Genome SHA-256
27ddef2fa602eb6c5c1e505a841619ac6f0d0b75c317f3144d9ea30a7be524c8
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': 474943, 'routing_taxid_rank': 'family', 'flags': ['identical_to_reference'], '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 474943', 'routed_by': 'family taxid 474943 (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
2026-11-07T02:17:01Z
Run time
66 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