MATPredict · mating-type report

OpiceaeUAMH11346

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 01:48 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 KE148160MAT1-2 locus: genes from left to right on KE148160, 377,999 to 415,153: APN2 (conserved flank, plus strand); COX13 (conserved flank, plus strand); MAT1-1-3 (core MAT gene, minus strand); MAT1-2-1 (core MAT gene, minus strand); MAT1-1-1 (core MAT gene, plus strand); SLA2 (conserved flank, minus strand).380 kb390 kb400 kb410 kb214.0 kb more to contig end →called locusAPN2: conserved flank, 377,999–380,603 (+), identity 63.6%, search hit onlyAPN2COX13: conserved flank, 385,195–385,881 (+), identity 64.4%, search hit onlyCOX13MAT1-1-3: core MAT gene, 406,396–407,379 (-), identity 35.3%, search hit onlyMAT1-1-3 (lost to MAT1-2-1)MAT1-2-1: core MAT gene, 406,396–407,379 (-), identity 75.9%, search hit onlyMAT1-2-1MAT1-1-1: core MAT gene, 408,629–409,863 (+), identity 39.2%, search hit onlyMAT1-1-1SLA2: conserved flank, 411,760–415,153 (-), identity 97.4%, search hit onlySLA2
Gene order on KE148160. Scroll sideways to see the whole figure.
FungiDB release 68 gene models on KE148160, 376,144 to 417,012F503_03618 373,927-377,007 (+): Zn(2)-C6 fungal-type domain-containing protein [Source:UniProtKB/TrEMBL;Acc:S3BYJ6]F503_03618F503_03619 377,999-380,603 (+): Apurinic-apyrimidinic endonuclease 2 [Source:UniProtKB/TrEMBL;Acc:S3BVH3]F503_03619F503_03620 381,081-382,891 (-): RING-type domain-containing protein [Source:UniProtKB/TrEMBL;Acc:S3CDY4]F503_03620F503_03621 385,195-385,881 (+): Cytochrome c oxidase subunit [Source:UniProtKB/TrEMBL;Acc:S3BTG1]F503_03621F503_03622 386,827-390,055 (-): unspecified productF503_03622F503_03623 399,269-401,086 (+): unspecified productF503_03623F503_03624 401,132-402,100 (+): unspecified productF503_03624F503_03625 406,396-407,379 (-): HMG box domain-containing protein [Source:UniProtKB/TrEMBL;Acc:S3CDY9]F503_03625F503_03626 408,629-409,863 (+): Mat1-1-1 [Source:UniProtKB/TrEMBL;Acc:S3BTG5]F503_03626F503_03627 411,760-415,153 (-): Cytoskeleton assembly control protein sla2 [Source:UniProtKB/TrEMBL;Acc:S3CUZ4]F503_03627F503_03628 415,910-420,997 (+): DNA polymerase [Source:UniProtKB/TrEMBL;Acc:S3BYK4]F503_03628
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
  • conserved flank
  • search hit only
Location
KE148160:377,999–415,153 · 37.2 kb
Own genes
KE148160:377,999–415,153 · 37.2 kb
Locus
Genes of both idiomorphs at one locus.
Genes modelled
5 of 6 gene hits
Nearest contig end
215.9 kb
Region (samtools)
KE148160:377999-415153
Idiomorph scores
  • MAT1-2 407.0
  • MAT1-1 183.0

Margin over the next idiomorph: 224.0

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
MAT1-2-175.9MAT1-1-335.3100.0higher identity

Gene evidence

GeneRoleModel Identity %E-value Position (strand)Exons Reference recordFungiDB gene
APN2conserved flankhit onlyDIAMOND, proteome63.6cov 84.6%4.5e-110341 bits377,999–380,603 +–27339_unknown-1_MAT_MAT1-2F503_03619
COX13conserved flankhit onlyDIAMOND, proteome64.4cov 67.9%5.8e-49146 bits385,195–385,881 +–5158_cbs114723_MAT_unswitchedF503_03621
MAT1-1-3core MATlost to MAT1-2-1, not countedhit onlyDIAMOND, proteome35.3cov 44.4%4.8e-1359 bits406,396–407,379 -–230073_uamh-1363_MAT_MAT1-1F503_03625
MAT1-2-1core MAThit onlyDIAMOND, proteome75.9cov 100.0%2.0e-147407 bits406,396–407,379 -–230073_uamh-11059_MAT_MAT1-2F503_03625
MAT1-1-1core MAThit onlyDIAMOND, proteome39.2cov 46.4%3.7e-54183 bits408,629–409,863 +–230073_uamh-1363_MAT_MAT1-1F503_03626
SLA2conserved flankhit onlyDIAMOND, proteome97.4cov 100.0%< 1e-1801,217 bits411,760–415,153 -–230073_uamh-1363_MAT_MAT1-1F503_03627

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
MATKE148165:394,280–397,529MAT1-2MAT1-2-11too few of the family's genes found

Provenance

Genome file
OpiceaeUAMH11346.genome.fasta
Assembly
45 contigs · 32.8 Mb · N50 1.5 Mb
Genome SHA-256
b246bf229cde14660adcdaa525a3733153d9a4483ffdfe47d52bae070cc4fd02
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': 5152, '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 5152', 'routed_by': 'family taxid 5152 (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
2026-11-07T01:47:04Z
Run time
64 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