MATPredict · mating-type report

PjiroveciiRU7

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 02:03 UTC by MATPredict 0.8.1

Result

Mating type

Mhigh confidence

Called loci 1

M PM family · Ascomycota

high confidence
Gene order of the M locus on LFWA01000009M locus: genes from left to right on LFWA01000009, 211,240 to 221,394: matPi (core MAT gene, minus strand); matMc (core MAT gene, minus strand); matMi (core MAT gene, plus strand).212 kb214 kb216 kb218 kb220 kb201.7 kb more to contig end →called locusmatPi: core MAT gene, 211,240–211,935 (-), identity 100.0%, search hit onlymatPimatMc: core MAT gene, 220,321–221,076 (-), identity 100.0%, search hit onlymatMcmatMi: core MAT gene, 221,185–221,394 (+), identity 100.0%, gene modelmatMi
Gene order on LFWA01000009. Scroll sideways to see the whole figure.
FungiDB release 68 gene models on LFWA01000009, 210,732 to 221,901T551_02159 211,240-211,935 (-): Homeobox domain-containing protein [Source:UniProtKB/TrEMBL;Acc:A0A0W4ZME4]T551_02159T551_02160 212,197-215,915 (+): ATP-dependent chaperone ClpBT551_02160T551_02161 215,418-219,678 (+): unspecified productT551_02161T551_02162 220,321-221,076 (-): HMG box domain-containing protein [Source:UniProtKB/TrEMBL;Acc:A0A0W4ZME2]T551_02162
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
  • gene model
  • search hit only
Location
LFWA01000009:211,240–221,394 · 10.2 kb
Cross-lineage class
MAT1-2
Own genes
LFWA01000009:211,240–221,394 · 10.2 kb
Locus
Genes of both idiomorphs at one locus.
Genes modelled
3 of 3 gene hits
Nearest contig end
202.2 kb
Region (samtools)
LFWA01000009:211240-221394
Idiomorph scores
  • M 477.0
  • P 455.0

Margin over the next idiomorph: 22.0

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, proteome100.0cov 100.0%2.0e-169455 bits211,240–211,935 -–42068_ru7_PM_combinedT551_02159
matMccore MAThit onlyDIAMOND, proteome100.0cov 100.0%1.9e-177477 bits220,321–221,076 -–42068_ru7_PM_combinedT551_02162
matMicore MATgene modelexonerate100.0cov 100.0%1.3e-39135 bits221,185–221,394 +142068_ru7_PM_combinednone
matPcnot searchable: no reference protein in the database–

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: fewer than 2 genes could be modelled (1).

Show the 1 withheld locus

Withheld loci (1)

familylocationidiomorph genesmodelledreason
PMLFWA01000002:31,619–31,753MmatMi0fewer than 2 genes could be modelled

Provenance

Genome file
PjiroveciiRU7.genome.fasta
Assembly
70 contigs · 8.4 Mb · N50 454.6 kb
Genome SHA-256
eb8c00b6dea5e42029c12e04f8bf83ae318f5068f7e43c2efe43ee9450f76106
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
2026-11-07T02:03:03Z
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