MATPredict · mating-type report

Pwakefieldiae2A

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 02:45 UTC by MATPredict 0.8.1

Result

Mating type

Pmedium confidence

Called loci 1

P PM family · Ascomycota

medium confidence
Gene order of the P locus on CP054543P locus: genes from left to right on CP054543, 71,161 to 81,241: matPi (core MAT gene, minus strand); matMc (core MAT gene, minus strand).72 kb74 kb76 kb78 kb80 kb← 70.7 kb more to contig endcalled locusmatPi: core MAT gene, 71,161–71,925 (-), identity 91.5%, search hit onlymatPimatMc: core MAT gene, 79,975–81,241 (-), identity 76.3%, search hit onlymatMc
Gene order on CP054543. Scroll sideways to see the whole figure.
FungiDB release 71 gene models on CP054543, 70,657 to 81,745MERGE_000829 70,357-70,883 (+): Prefoldin subunit | domain-containing proteinMERGE_000829MERGE_000830 71,161-71,925 (-): Homeobox KN domain | domain-containing proteinMERGE_000830MERGE_000831 72,029-79,513 (+): C-terminal, D2-small domain, of ClpB protein | ATPase family associated with various cellular activities (AAA) | Clp amino terminal domain, pathogenicity island component | AAA domain (Cdc48 subfamily) | AAA lid domain | ANTH domain | I/LWEQ domain | domain-containing proteinMERGE_000831MERGE_000832 79,975-81,241 (-): HMG (high mobility group) box | domain-containing proteinMERGE_000832MERGE_000833 81,482-82,376 (+): Homeodomain | domain-containing proteinMERGE_000833
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
  • search hit only
Location
CP054543:71,161–81,241 · 10.1 kb
Cross-lineage class
unassigned
Own genes
CP054543:71,161–81,241 · 10.1 kb
Locus
Genes of both idiomorphs at one locus.
Genes modelled
2 of 2 gene hits
Nearest contig end
71.2 kb
Region (samtools)
CP054543:71161-81241
Idiomorph scores
  • P 384.0
  • M 336.0

Margin over the next idiomorph: 48.0

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

Gene evidence

GeneRoleModel Identity %E-value Position (strand)Exons Reference recordFungiDB gene
matPicore MAThit onlyDIAMOND, proteome91.5cov 91.7%1.9e-141384 bits71,161–71,925 -–4754_b80_PM_combinedMERGE_000830
matMccore MAThit onlyDIAMOND, proteome76.3cov 100.0%6.7e-122336 bits79,975–81,241 -–4754_b80_PM_combinedMERGE_000832
matMiexpected, not found–
matPcnot searchable: no reference protein in the database–

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: fewer than 2 genes could be modelled (2).

Show the 2 withheld loci

Withheld loci (2)

familylocationidiomorph genesmodelledreason
PMCP054547:27,900–28,001MmatMi0fewer than 2 genes could be modelled
PMCP054537:234,061–234,159MmatMi0fewer than 2 genes could be modelled

Provenance

Genome file
Pwakefieldiae2A.genome.fasta
Assembly
17 contigs · 7.3 Mb · N50 480.7 kb
Genome SHA-256
83d78ddabfc882895a80f67895aa6365e90965ed0202a62841b96a12b9b1e738
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': 44281, 'routing_taxid_rank': 'family', 'flags': ['short_genome', '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 44281', 'routed_by': 'family taxid 44281 (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, supported_min_bitscore=33.0
Run started
2026-11-07T02:45:34Z
Run time
11 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