MATPredict · mating-type report

PblakesleeanusNRRL1555

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 01:52 UTC by MATPredict 0.8.1

Result

Mating type

Minushigh confidence

Called loci 1

Minus MAT family · Mucoromycota

high confidence
Gene order of the Minus locus on KV440971Minus locus: genes from left to right on KV440971, 3,978,271 to 3,991,613: algA (variable flank, minus strand); tptA (conserved flank, minus strand); sexM (core MAT gene, plus strand); sexP (core MAT gene, plus strand); rnhA (conserved flank, plus strand).3,980 kb3,985 kb3,990 kb460.2 kb more to contig end →called locusalgA: variable flank, 3,978,271–3,979,861 (-), identity 48.5%, search hit onlyalgAtptA: conserved flank, 3,980,891–3,983,141 (-), identity 100.0%, search hit onlytptAsexM: core MAT gene, 3,985,605–3,986,240 (+), identity 100.0%, search hit onlysexMsexP: core MAT gene, 3,985,731–3,985,973 (+), identity 35.8%, gene modelsexP (lost to sexM)rnhA: conserved flank, 3,986,572–3,991,613 (+), identity 99.8%, search hit onlyrnhA
Gene order on KV440971. Scroll sideways to see the whole figure.
FungiDB release 68 gene models on KV440971, 3,977,604 to 3,992,279PHYBLDRAFT_80073 3,978,197-3,979,861 (-): Alginate lyase domain-containing protein [Source:UniProtKB/TrEMBL;Acc:A0A162QAJ1]PHYBLDRAFT_80073PHYBLDRAFT_184619 3,980,647-3,983,141 (-): Sugar phosphate transporter domain-containing protein [Source:UniProtKB/TrEMBL;Acc:A0A167RE66]PHYBLDRAFT_184619PHYBLDRAFT_154054 3,985,605-3,986,240 (+): HMG box domain-containing protein [Source:UniProtKB/TrEMBL;Acc:A0A167RE73]PHYBLDRAFT_154054PHYBLDRAFT_80075 3,986,572-3,991,627 (+): RNA helicase [Source:UniProtKB/TrEMBL;Acc:A0A167RGN6]PHYBLDRAFT_80075
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
  • variable flank
  • gene model
  • search hit only
  • sexP is a weak hit to the other idiomorph's gene and was not counted against the call.
Location
KV440971:3,978,271–3,991,613 · 13.3 kb
Own genes
KV440971:3,978,271–3,991,613 · 13.3 kb
Locus
Complete locus: MAT gene(s) with their flanking genes.
Genes modelled
4 of 5 gene hits
Nearest contig end
460.8 kb
Region (samtools)
KV440971:3978271-3991613
Idiomorph scores
  • Minus 134.1
  • Plus 63.3

Margin over the next idiomorph: 70.8

Score: HMM bitscore of the MAT protein against each idiomorph's profile.

Profile-HMM classifier
  • Minus 134.1
  • Plus 63.3

Margin 70.8 (a call needs 25.0 or more). Scored: sexP (model).

Overlapping hits resolved

Where genes of two idiomorphs hit the same place, the stronger hit was kept.

keptidentity %set asideidentity %overlap %basis
sexM100.0sexP34.7100.0higher identity

Gene evidence

GeneRoleModel Identity %E-value Position (strand)Exons Reference recordFungiDB gene
algAvariable flankhit onlyDIAMOND, proteome48.5cov 99.5%3.5e-127365 bits3,978,271–3,979,861 -–3108396_ai-2023a_MAT_PlusPHYBLDRAFT_80073
tptAconserved flankhit onlyDIAMOND, proteome100.0cov 100.0%8.2e-202556 bits3,980,891–3,983,141 -–4837_nrrl1555_MAT_MinusPHYBLDRAFT_184619
sexMcore MAThit onlyDIAMOND, proteome100.0cov 100.0%4.1e-152413 bits3,985,605–3,986,240 +–4837_nrrl1555_MAT_MinusPHYBLDRAFT_154054
sexPcore MATother idiomorph, not countedlost to sexM, not countedgene modelexonerate35.8cov 27.3%2.6e-1165 bits3,985,731–3,985,973 +14837_ubc21_MAT_PlusPHYBLDRAFT_154054
rnhAconserved flankhit onlyDIAMOND, proteome99.8cov 98.2%< 1e-1801,285 bits3,986,572–3,991,613 +–4837_nrrl1555_MAT_MinusPHYBLDRAFT_80075
glrAexpected, not found–

Withheld candidate loci 11

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 (11).

Show the 11 withheld loci

Withheld loci (11)

familylocationidiomorph genesmodelledreason
MATKV440972:2,030,804–2,039,253undeterminedsexP, glrA1too few of the family's genes found
MATKV440975:1,395,401–1,397,256undeterminedrnhA1too few of the family's genes found
MATKV440976:1,000,676–1,002,428undeterminedsexP1too few of the family's genes found
MATKV440985:721,906–723,701undeterminedglrA1too few of the family's genes found
MATKV440987:149,620–150,951undeterminedtptA1too few of the family's genes found
MATKV440990:987,879–989,068undeterminedsexM1too few of the family's genes found
MATKV440991:852,866–858,822undeterminedbtbA1too few of the family's genes found
MATKV440996:637,622–643,033undeterminedrnhA1too few of the family's genes found
MATKV440997:469,288–470,528PlussexP1too few of the family's genes found
MATKV440999:139,633–141,163undeterminedtptA1too few of the family's genes found
MATKV441000:289,935–293,987undeterminedrnhA1too few of the family's genes found

Provenance

Genome file
PblakesleeanusNRRL1555.genome.fasta
Assembly
80 contigs · 53.9 Mb · N50 1.5 Mb
Genome SHA-256
da5cbaca37236ecc8fe32980e0eaee9fcebe8dbe828f4fc337bdfce027ba3d33
MATPredict
0.8.1 (v0.8.1, 3a62e6302b)
Database
86f18d232e4fe95d · 185 records
Taxonomy
local NCBI taxonomy snapshot 2026-10-01
Parameters
phylum=Mucoromycota, phylum_guess={'requested': 'auto', 'status': 'ok', 'usable': True, 'reason': None, 'phylum': 'Mucoromycota', 'phylum_taxid': 1913637, 'deepest_rank': 'species', 'routing_taxid': 1344966, 'routing_taxid_rank': 'family', 'flags': [], '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 Mucoromycota', 'action': 'routed', 'weak_call_accepted': False, 'genetic_code': 1, 'genetic_code_from': 'family taxid 1344966', 'routed_by': 'family taxid 1344966 (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
2026-11-07T01:51:44Z
Run time
46 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