MATPredict · mating-type report

RtoruloidesNBRC0880

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 02:53 UTC by MATPredict 0.8.1

Result

Mating-type loci

undeterminedredHDhigh confidenceA2redPRhigh confidence

Called loci 2

undetermined redHD family · Basidiomycota

high confidence
Gene order of the undetermined locus on LCTV02000005undetermined locus: genes from left to right on LCTV02000005, 1,270,620 to 1,276,279: HD1 (core MAT gene, minus strand); HD2 (core MAT gene, plus strand).1,271 kb1,272 kb1,273 kb1,274 kb1,275 kb1,276 kb390.1 kb more to contig end →called locusHD1: core MAT gene, 1,270,620–1,271,852 (-), identity 100.0%, search hit onlyHD1HD2: core MAT gene, 1,272,303–1,276,279 (+), identity 98.5%, search hit onlyHD2
Gene order on LCTV02000005. Scroll sideways to see the whole figure.
FungiDB release 71 gene models on LCTV02000005, 1,270,320 to 1,276,579AAT19DRAFT_14302 1,268,889-1,270,479 (-): Mitochondrial carrier protein | domain-containing proteinAAT19DRAFT_14302AAT19DRAFT_14303 1,270,620-1,271,852 (-): Homeobox KN domain | domain-containing proteinAAT19DRAFT_14303AAT19DRAFT_14304 1,272,303-1,276,279 (+): Proteophosphoglycan 5AAT19DRAFT_14304AAT19DRAFT_14305 1,276,566-1,277,864 (+): unspecified productAAT19DRAFT_14305
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
  • Idiomorph undetermined: the evidence for two idiomorphs is tied or too close to call.
Location
LCTV02000005:1,270,620–1,276,279 · 5.7 kb
Own genes
LCTV02000005:1,270,620–1,276,279 · 5.7 kb
Locus
A MAT gene with no flanking gene beside it; not a full locus.
Genes modelled
2 of 2 gene hits
Nearest contig end
390.4 kb
Region (samtools)
LCTV02000005:1270620-1276279

Gene evidence

GeneRoleModel Identity %E-value Position (strand)Exons Reference recordFungiDB gene
HD1core MAThit onlyDIAMOND, proteome100.0cov 100.0%3.0e-298798 bits1,270,620–1,271,852 -–5286_nbrc-0880_redHD_B39AAT19DRAFT_14303
HD2core MAThit onlyDIAMOND, proteome98.5cov 99.1%2.9e-225637 bits1,272,303–1,276,279 +–5286_nbrc-0880_redHD_B39AAT19DRAFT_14304

A2 redPR family · Basidiomycota

high confidence
Gene order of the A2 locus on LCTV02000013A2 locus: genes from left to right on LCTV02000013, 476,602 to 479,053: STE3a1 (core MAT gene, minus strand); STE3a2 (core MAT gene, minus strand); RibL6 (conserved flank, minus strand).476.5 kb477.0 kb477.5 kb478.0 kb478.5 kb479.0 kb305.5 kb more to contig end →called locusSTE3a1: core MAT gene, 476,602–477,940 (-), identity 31.3%, search hit onlySTE3a1 (lost to STE3a2)STE3a2: core MAT gene, 476,602–477,940 (-), identity 100.0%, search hit onlySTE3a2RibL6: conserved flank, 478,240–479,053 (-), identity 60.6%, search hit onlyRibL6
Gene order on LCTV02000013. Scroll sideways to see the whole figure.
FungiDB release 71 gene models on LCTV02000013, 476,302 to 479,353AAT19DRAFT_10625 475,643-476,566 (+): Like-Sm (LSM) domain-containing proteinAAT19DRAFT_10625AAT19DRAFT_10626 476,567-478,033 (-): pheromone receptor mating-type A2AAT19DRAFT_10626AAT19DRAFT_10627 478,240-479,053 (-): putative ribosomal protein L6AAT19DRAFT_10627AAT19DRAFT_10628 479,323-480,652 (+): DNA-directed RNA polymerases I and III subunit RPAC1AAT19DRAFT_10628
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
  • STE3a1 is a weak hit to the other idiomorph's gene and was not counted against the call.
Location
LCTV02000013:476,602–479,053 · 2.5 kb
Own genes
LCTV02000013:476,602–479,053 · 2.5 kb
Locus
Complete locus: MAT gene(s) with their flanking genes.
Genes modelled
2 of 3 gene hits
Nearest contig end
305.8 kb
Region (samtools)
LCTV02000013:476602-479053
Idiomorph scores
  • A2 704.0

Margin over the set-aside STE3a1 hit: 68.7 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
STE3a2100.0STE3a131.3100.0higher identity

Gene evidence

GeneRoleModel Identity %E-value Position (strand)Exons Reference recordFungiDB gene
STE3a1core MATother idiomorph, not countedlost to STE3a2, not countedhit onlyDIAMOND, proteome31.3cov 76.6%3.3e-50163 bits476,602–477,940 -–5286_cbs-14_redPR_A1AAT19DRAFT_10626
STE3a2core MAThit onlyDIAMOND, proteome100.0cov 100.0%3.9e-263704 bits476,602–477,940 -–5286_nbrc-0880_redPR_A2AAT19DRAFT_10626
RibL6conserved flankhit onlyDIAMOND, proteome60.6cov 93.8%6.2e-85244 bits478,240–479,053 -–217517_cbs-9654_redPR_A2AAT19DRAFT_10627

Provenance

Genome file
RtoruloidesNBRC0880.genome.fasta
Assembly
30 contigs · 20.7 Mb · N50 1.4 Mb
Genome SHA-256
f15fa1fcb15e49fc00418dbaec8847a829ab459b16212458dc714820b7c6d3ad
MATPredict
0.8.1 (v0.8.1, 3a62e6302b)
Database
86f18d232e4fe95d · 185 records
Taxonomy
local NCBI taxonomy snapshot 2026-10-01
Parameters
phylum=Basidiomycota, phylum_guess={'requested': 'auto', 'status': 'ok', 'usable': True, 'reason': None, 'phylum': 'Basidiomycota', 'phylum_taxid': 5204, 'deepest_rank': 'genus', 'routing_taxid': 1799696, '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 Basidiomycota', 'action': 'routed', 'weak_call_accepted': False, 'genetic_code': 1, 'genetic_code_from': 'family taxid 1799696', 'routed_by': 'family taxid 1799696 (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
2026-11-07T02:53:22Z
Run time
9 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