MATPredict · mating-type report

MpachydermatisCBS1879

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 01:54 UTC by MATPredict 0.8.1

Result

Mating-type loci

undeterminedaLocushigh confidenceundeterminedbLocushigh confidence

Called loci 2

undetermined aLocus family · Basidiomycota

high confidence
Gene order of the undetermined locus on LGAV01000001undetermined locus: genes from left to right on LGAV01000001, 1,018,608 to 1,020,377: mfa1 (core MAT gene, minus strand); pra1 (core MAT gene, plus strand).1,018.5 kb1,019.0 kb1,019.5 kb1,020.0 kb1,020.5 kb468.4 kb more to contig end →called locusmfa1: core MAT gene, 1,018,608–1,018,757 (-), identity 50.0%, gene modelmfa1pra1: core MAT gene, 1,019,422–1,020,377 (+), identity 26.0%, search hit onlypra1
Gene order on LGAV01000001. Scroll sideways to see the whole figure.
FungiDB release 68 gene models on LGAV01000001, 1,018,308 to 1,020,677Malapachy_3468 1,019,422-1,020,377 (+): pheromone receptor a1Malapachy_3468Malapachy_3453 1,020,500-1,021,679 (-): 26s proteasome regulatory subunit rpn10Malapachy_3453
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
  • Idiomorph undetermined: the evidence for two idiomorphs is tied or too close to call.
Location
LGAV01000001:1,018,608–1,020,377 · 1.8 kb
Own genes
LGAV01000001:1,018,608–1,020,377 · 1.8 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
468.7 kb
Region (samtools)
LGAV01000001:1018608-1020377

Gene evidence

GeneRoleModel Identity %E-value Position (strand)Exons Reference recordFungiDB gene
mfa1core MATgene modelexonerate50.0cov 100.0%1.3e-1155 bits1,018,608–1,018,757 -176777_unspecified-a1_aLocus_a1none
pra1core MAThit onlyDIAMOND, proteome26.0cov 60.8%3.1e-2184 bits1,019,422–1,020,377 +–394055_cbs-10428_aLocus_a1Malapachy_3468
rba1expected, not found–

undetermined bLocus family · Basidiomycota

high confidence
Gene order of the undetermined locus on LGAV01000004undetermined locus: genes from left to right on LGAV01000004, 366,673 to 372,093: bW (core MAT gene, minus strand); bE (core MAT gene, plus strand).367 kb368 kb369 kb370 kb371 kb372 kb← 366.4 kb more to contig endcalled locusbW: core MAT gene, 366,673–369,885 (-), identity 78.4%, search hit onlybWbE: core MAT gene, 371,524–372,093 (+), identity 44.2%, search hit onlybE
Gene order on LGAV01000004. Scroll sideways to see the whole figure.
FungiDB release 68 gene models on LGAV01000004, 366,373 to 372,393Malapachy_3903 365,468-366,484 (-): NADP-dependent oxidoreductase domain-containing protein [Source:UniProtKB/TrEMBL;Acc:A0A0M8MVM1]Malapachy_3903Malapachy_3924 366,673-369,885 (-): high-affinity methionine permeaseMalapachy_3924Malapachy_3918 370,563-371,465 (+): homeodomain transcription factor beMalapachy_3918Malapachy_3919 371,524-372,093 (+): Exosome complex protein [Source:UniProtKB/TrEMBL;Acc:A0A0M8MV79]Malapachy_3919Malapachy_3909 372,244-373,995 (+): unspecified productMalapachy_3909
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
  • search hit only
  • Idiomorph undetermined: the evidence for two idiomorphs is tied or too close to call.
Location
LGAV01000004:366,673–372,093 · 5.4 kb
Own genes
LGAV01000004:366,673–372,093 · 5.4 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
366.7 kb
Region (samtools)
LGAV01000004:366673-372093

Gene evidence

GeneRoleModel Identity %E-value Position (strand)Exons Reference recordFungiDB gene
bWcore MAThit onlyDIAMOND, proteome78.4cov 8.0%3.5e-45163 bits366,673–369,885 -–327079_sy62_bLocus_b1Malapachy_3924
bEcore MAThit onlyDIAMOND, proteome44.2cov 16.4%4.1e-72217 bits371,524–372,093 +–349360_cbs-131475_bLocus_b1Malapachy_3919

Withheld candidate loci 75

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 (75).

Show the 75 withheld loci

Withheld loci (75)

familylocationidiomorph genesmodelledreason
bLocusLGAV01000001:257,074–257,367undeterminedbE0fewer than 2 genes could be modelled
bLocusLGAV01000001:287,757–287,963undeterminedbE0fewer than 2 genes could be modelled
bLocusLGAV01000001:347,923–348,033undeterminedbE0fewer than 2 genes could be modelled
bLocusLGAV01000001:463,736–465,116undeterminedbE, bW1fewer than 2 genes could be modelled
bLocusLGAV01000001:607,565–607,837undeterminedbE0fewer than 2 genes could be modelled
bLocusLGAV01000001:799,362–799,514undeterminedbE0fewer than 2 genes could be modelled
bLocusLGAV01000001:865,372–865,503undeterminedbE0fewer than 2 genes could be modelled
bLocusLGAV01000001:882,472–882,642undeterminedbE0fewer than 2 genes could be modelled
bLocusLGAV01000001:907,186–907,326undeterminedbE0fewer than 2 genes could be modelled
bLocusLGAV01000001:944,886–945,053undeterminedbE0fewer than 2 genes could be modelled
bLocusLGAV01000001:967,605–967,895undeterminedbE0fewer than 2 genes could be modelled
bLocusLGAV01000001:1,238,414–1,238,590undeterminedbE0fewer than 2 genes could be modelled
bLocusLGAV01000001:1,313,514–1,313,603undeterminedbE0fewer than 2 genes could be modelled
bLocusLGAV01000001:1,372,565–1,372,702undeterminedbE0fewer than 2 genes could be modelled
bLocusLGAV01000004:76,853–76,951undeterminedbE0fewer than 2 genes could be modelled
bLocusLGAV01000004:171,597–171,743undeterminedbE0fewer than 2 genes could be modelled
bLocusLGAV01000004:284,348–284,461undeterminedbE0fewer than 2 genes could be modelled
bLocusLGAV01000004:353,708–353,896undeterminedbE0fewer than 2 genes could be modelled
bLocusLGAV01000004:446,126–446,407undeterminedbE0fewer than 2 genes could be modelled
bLocusLGAV01000004:546,824–546,949undeterminedbE0fewer than 2 genes could be modelled
bLocusLGAV01000004:647,002–647,124undeterminedbE0fewer than 2 genes could be modelled
bLocusLGAV01000004:810,190–810,342undeterminedbE0fewer than 2 genes could be modelled
bLocusLGAV01000004:835,437–835,550undeterminedbE0fewer than 2 genes could be modelled
bLocusLGAV01000004:859,434–859,547undeterminedbE0fewer than 2 genes could be modelled
bLocusLGAV01000004:868,600–868,785undeterminedbE0fewer than 2 genes could be modelled
bLocusLGAV01000004:904,707–904,997undeterminedbE0fewer than 2 genes could be modelled
bLocusLGAV01000004:918,469–919,878undeterminedbE0fewer than 2 genes could be modelled
bLocusLGAV01000007:109,584–109,784undeterminedbE0fewer than 2 genes could be modelled
bLocusLGAV01000007:311,814–311,984undeterminedbE0fewer than 2 genes could be modelled
bLocusLGAV01000007:347,275–347,742undeterminedbE0fewer than 2 genes could be modelled
bLocusLGAV01000007:369,389–371,446undeterminedbE0fewer than 2 genes could be modelled
bLocusLGAV01000007:407,490–407,675undeterminedbE0fewer than 2 genes could be modelled
bLocusLGAV01000007:419,336–419,578undeterminedbE0fewer than 2 genes could be modelled
bLocusLGAV01000007:535,771–536,691undeterminedbE0fewer than 2 genes could be modelled
bLocusLGAV01000007:544,824–545,174undeterminedbE0fewer than 2 genes could be modelled
bLocusLGAV01000002:100,017–100,286undeterminedbE0fewer than 2 genes could be modelled
bLocusLGAV01000002:217,640–219,975undeterminedbE0fewer than 2 genes could be modelled
bLocusLGAV01000002:305,934–306,266undeterminedbE0fewer than 2 genes could be modelled
bLocusLGAV01000002:335,129–335,293undeterminedbE0fewer than 2 genes could be modelled
bLocusLGAV01000002:355,837–356,079undeterminedbE0fewer than 2 genes could be modelled
bLocusLGAV01000002:413,990–414,130undeterminedbE0fewer than 2 genes could be modelled
bLocusLGAV01000002:452,799–453,002undeterminedbE0fewer than 2 genes could be modelled
bLocusLGAV01000002:525,797–526,719undeterminedbE0fewer than 2 genes could be modelled
bLocusLGAV01000002:533,726–533,845undeterminedbE0fewer than 2 genes could be modelled
bLocusLGAV01000002:748,733–748,873undeterminedbE0fewer than 2 genes could be modelled
bLocusLGAV01000002:770,547–770,639undeterminedbE0fewer than 2 genes could be modelled
bLocusLGAV01000002:875,840–876,304undeterminedbE0fewer than 2 genes could be modelled
bLocusLGAV01000002:1,073,661–1,073,834undeterminedbE0fewer than 2 genes could be modelled
bLocusLGAV01000009:104,686–104,871undeterminedbE0fewer than 2 genes could be modelled
bLocusLGAV01000008:253,565–253,858undeterminedbE0fewer than 2 genes could be modelled
bLocusLGAV01000003:136,749–136,856undeterminedbE0fewer than 2 genes could be modelled
bLocusLGAV01000003:205,767–205,919undeterminedbE0fewer than 2 genes could be modelled
bLocusLGAV01000003:400,311–400,409undeterminedbE0fewer than 2 genes could be modelled
bLocusLGAV01000003:500,586–500,702undeterminedbE0fewer than 2 genes could be modelled
bLocusLGAV01000003:568,372–568,587undeterminedbE0fewer than 2 genes could be modelled
bLocusLGAV01000003:873,535–873,822undeterminedbE0fewer than 2 genes could be modelled
bLocusLGAV01000003:897,973–898,068undeterminedbE0fewer than 2 genes could be modelled
bLocusLGAV01000003:1,264,255–1,264,437undeterminedbE0fewer than 2 genes could be modelled
bLocusLGAV01000005:23,099–26,411undeterminedbE0fewer than 2 genes could be modelled
bLocusLGAV01000005:96,574–96,816undeterminedbE0fewer than 2 genes could be modelled
bLocusLGAV01000005:223,735–224,082undeterminedbE0fewer than 2 genes could be modelled
bLocusLGAV01000005:270,606–270,773undeterminedbE0fewer than 2 genes could be modelled
bLocusLGAV01000005:411,020–411,154undeterminedbE0fewer than 2 genes could be modelled
bLocusLGAV01000005:483,091–483,222undeterminedbE0fewer than 2 genes could be modelled
bLocusLGAV01000005:493,648–493,842undeterminedbE0fewer than 2 genes could be modelled
bLocusLGAV01000005:501,928–502,236undeterminedbE0fewer than 2 genes could be modelled
bLocusLGAV01000011:123,419–123,622undeterminedbE0fewer than 2 genes could be modelled
bLocusLGAV01000011:147,795–151,820undeterminedbE0fewer than 2 genes could be modelled
bLocusLGAV01000011:157,732–158,025undeterminedbE0fewer than 2 genes could be modelled
bLocusLGAV01000011:163,178–163,273undeterminedbE0fewer than 2 genes could be modelled
bLocusLGAV01000013:46,528–50,224undeterminedbE0fewer than 2 genes could be modelled
bLocusLGAV01000010:46,994–47,092undeterminedbE0fewer than 2 genes could be modelled
bLocusLGAV01000014:7,235–7,519undeterminedbE0fewer than 2 genes could be modelled
bLocusLGAV01000006:493,664–493,786undeterminedbE0fewer than 2 genes could be modelled
bLocusLGAV01000006:547,238–547,776undeterminedbE0fewer than 2 genes could be modelled

Provenance

Genome file
MpachydermatisCBS1879.genome.fasta
Assembly
91 contigs · 8.2 Mb · N50 1.3 Mb
Genome SHA-256
26c6def55961017e003b0bf568d976f7baaa47b5ef6c9c5a0f23ac6dbc4209d3
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': 'species', 'routing_taxid': 742845, '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 742845', 'routed_by': 'family taxid 742845 (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
2026-11-07T01:53:51Z
Run time
27 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