MATPredict · mating-type report

MsympodialisATCC42132

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 02:37 UTC by MATPredict 0.8.1

Result

Mating-type loci

undeterminedbLocushigh confidenceundeterminedaLocushigh confidence

Called loci 2

undetermined bLocus family · Basidiomycota

high confidence
Gene order of the undetermined locus on LT671821undetermined locus: genes from left to right on LT671821, 721,646 to 724,665: bW (core MAT gene, minus strand); bE (core MAT gene, plus strand).722 kb723 kb724 kb← 721.3 kb more to contig endcalled locusbW: core MAT gene, 721,646–723,292 (-), identity 96.0%, search hit onlybWbE: core MAT gene, 723,796–724,665 (+), identity 100.0%, search hit onlybE
Gene order on LT671821. Scroll sideways to see the whole figure.
FungiDB release 71 gene models on LT671821, 721,346 to 724,965MSYG_0446 721,252-723,460 (-): Homeodomain | domain-containing proteinMSYG_0446MSYG_0447 723,356-724,665 (+): Homeobox KN domain | domain-containing proteinMSYG_0447MSYG_0448 724,750-725,307 (+): Sas10/Utp3/C1D family | domain-containing proteinMSYG_0448
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
LT671821:721,646–724,665 · 3.0 kb
Own genes
LT671821:721,646–724,665 · 3.0 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
721.6 kb
Region (samtools)
LT671821:721646-724665

Gene evidence

GeneRoleModel Identity %E-value Position (strand)Exons Reference recordFungiDB gene
bWcore MAThit onlyDIAMOND, proteome96.0cov 100.0%< 1e-180994 bits721,646–723,292 -–76777_atcc-42132_bLocus_b1MSYG_0446
bEcore MAThit onlyDIAMOND, proteome100.0cov 100.0%7.4e-209563 bits723,796–724,665 +–76777_atcc-42132_bLocus_b1MSYG_0447

undetermined aLocus family · Basidiomycota

high confidence
Gene order of the undetermined locus on LT671821undetermined locus: genes from left to right on LT671821, 866,423 to 868,166: mfa1 (core MAT gene, minus strand); pra1 (core MAT gene, plus strand).866.5 kb867.0 kb867.5 kb868.0 kb640.5 kb more to contig end →called locusmfa1: core MAT gene, 866,423–866,572 (-), identity 100.0%, gene modelmfa1pra1: core MAT gene, 866,952–868,166 (+), identity 33.2%, search hit onlypra1
Gene order on LT671821. Scroll sideways to see the whole figure.
FungiDB release 71 gene models on LT671821, 866,123 to 868,466MSYG_0529 866,086-866,243 (+): unspecified productMSYG_0529MSYG_0530 866,784-868,378 (+): Pheromone A receptor | domain-containing proteinMSYG_0530MSYG_0531 868,027-869,403 (-): von Willebrand factor type A domain | Ubiquitin interaction motif | domain-containing proteinMSYG_0531
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
  • gene model
  • search hit only
  • Idiomorph undetermined: the evidence for two idiomorphs is tied or too close to call.
Location
LT671821:866,423–868,166 · 1.7 kb
Own genes
LT671821:866,423–868,166 · 1.7 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
640.8 kb
Region (samtools)
LT671821:866423-868166

Gene evidence

GeneRoleModel Identity %E-value Position (strand)Exons Reference recordFungiDB gene
mfa1core MATgene modelexonerate100.0cov 100.0%5.9e-29103 bits866,423–866,572 -176777_unspecified-a1_aLocus_a1none
pra1core MAThit onlyDIAMOND, proteome33.2cov 82.6%6.4e-52169 bits866,952–868,166 +–5270_521_aLocus_a1MSYG_0530
MSYG_0531 (opposite strand)
rba1expected, not found–

Withheld candidate loci 71

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 (71).

Show the 71 withheld loci

Withheld loci (71)

familylocationidiomorph genesmodelledreason
bLocusLT671821:14,111–14,257undeterminedbE0fewer than 2 genes could be modelled
bLocusLT671821:197,813–198,079undeterminedbE0fewer than 2 genes could be modelled
bLocusLT671821:219,667–219,876undeterminedbE0fewer than 2 genes could be modelled
bLocusLT671821:250,377–250,508undeterminedbE0fewer than 2 genes could be modelled
bLocusLT671821:399,500–399,880undeterminedbE0fewer than 2 genes could be modelled
bLocusLT671821:964,073–964,177undeterminedbE0fewer than 2 genes could be modelled
bLocusLT671821:1,102,388–1,102,513undeterminedbE0fewer than 2 genes could be modelled
bLocusLT671821:1,199,368–1,199,646undeterminedbE0fewer than 2 genes could be modelled
bLocusLT671821:1,345,292–1,345,396undeterminedbE0fewer than 2 genes could be modelled
bLocusLT671821:1,417,845–1,417,943undeterminedbE0fewer than 2 genes could be modelled
bLocusLT671826:124,187–124,336undeterminedbE0fewer than 2 genes could be modelled
bLocusLT671826:272,005–274,173undeterminedbW1fewer than 2 genes could be modelled
bLocusLT671826:287,754–287,912undeterminedbE0fewer than 2 genes could be modelled
bLocusLT671826:312,746–312,916undeterminedbE0fewer than 2 genes could be modelled
bLocusLT671826:366,967–367,170undeterminedbE0fewer than 2 genes could be modelled
bLocusLT671826:466,106–466,270undeterminedbE0fewer than 2 genes could be modelled
bLocusLT671826:608,206–608,421undeterminedbE0fewer than 2 genes could be modelled
bLocusLT671824:10,506–10,631undeterminedbE0fewer than 2 genes could be modelled
bLocusLT671824:31,297–34,678undeterminedbE0fewer than 2 genes could be modelled
bLocusLT671824:180,564–180,698undeterminedbE0fewer than 2 genes could be modelled
bLocusLT671824:299,202–299,321undeterminedbE0fewer than 2 genes could be modelled
bLocusLT671824:540,314–540,418undeterminedbE0fewer than 2 genes could be modelled
bLocusLT671824:619,669–619,908undeterminedbE0fewer than 2 genes could be modelled
bLocusLT671824:673,807–674,071undeterminedbE0fewer than 2 genes could be modelled
bLocusLT671824:803,144–803,368undeterminedbE0fewer than 2 genes could be modelled
bLocusLT671824:820,888–821,124undeterminedbE0fewer than 2 genes could be modelled
bLocusLT671824:906,026–906,151undeterminedbE0fewer than 2 genes could be modelled
bLocusLT671824:1,015,969–1,016,100undeterminedbE0fewer than 2 genes could be modelled
bLocusLT671824:1,157,838–1,157,957undeterminedbE0fewer than 2 genes could be modelled
bLocusLT671824:1,189,283–1,189,411undeterminedbE0fewer than 2 genes could be modelled
bLocusLT671827:86,296–86,427undeterminedbE0fewer than 2 genes could be modelled
bLocusLT671827:118,126–118,347undeterminedbE0fewer than 2 genes could be modelled
bLocusLT671827:250,751–251,038undeterminedbE0fewer than 2 genes could be modelled
bLocusLT671827:374,774–374,920undeterminedbE0fewer than 2 genes could be modelled
bLocusLT671827:403,310–403,471undeterminedbE0fewer than 2 genes could be modelled
bLocusLT671827:474,122–474,343undeterminedbE0fewer than 2 genes could be modelled
bLocusLT671823:2,999–3,235undeterminedbE0fewer than 2 genes could be modelled
bLocusLT671823:112,072–112,347undeterminedbE0fewer than 2 genes could be modelled
bLocusLT671823:171,275–171,445undeterminedbE0fewer than 2 genes could be modelled
bLocusLT671823:269,279–269,503undeterminedbE0fewer than 2 genes could be modelled
bLocusLT671823:505,487–505,603undeterminedbE0fewer than 2 genes could be modelled
bLocusLT671823:568,476–568,643undeterminedbE0fewer than 2 genes could be modelled
bLocusLT671823:713,214–713,309undeterminedbE0fewer than 2 genes could be modelled
bLocusLT671823:890,255–890,467undeterminedbE0fewer than 2 genes could be modelled
bLocusLT671823:933,717–933,833undeterminedbE0fewer than 2 genes could be modelled
bLocusLT671823:1,007,952–1,008,179undeterminedbE0fewer than 2 genes could be modelled
bLocusLT671823:1,242,981–1,243,103undeterminedbE0fewer than 2 genes could be modelled
bLocusLT671823:1,311,722–1,311,844undeterminedbE0fewer than 2 genes could be modelled
bLocusLT671828:116,758–116,970undeterminedbE0fewer than 2 genes could be modelled
bLocusLT671828:180,412–180,705undeterminedbE0fewer than 2 genes could be modelled
bLocusLT671828:332,209–332,379undeterminedbE0fewer than 2 genes could be modelled
bLocusLT671822:144,373–144,528undeterminedbE0fewer than 2 genes could be modelled
bLocusLT671822:154,137–154,229undeterminedbE0fewer than 2 genes could be modelled
bLocusLT671822:186,529–186,702undeterminedbE0fewer than 2 genes could be modelled
bLocusLT671822:347,267–347,371undeterminedbE0fewer than 2 genes could be modelled
bLocusLT671822:361,098–361,244undeterminedbE0fewer than 2 genes could be modelled
bLocusLT671822:520,879–521,142undeterminedbE0fewer than 2 genes could be modelled
bLocusLT671822:563,534–563,644undeterminedbE0fewer than 2 genes could be modelled
bLocusLT671822:613,711–614,004undeterminedbE0fewer than 2 genes could be modelled
bLocusLT671822:686,448–686,597undeterminedbE0fewer than 2 genes could be modelled
bLocusLT671822:939,084–944,346undeterminedbE0fewer than 2 genes could be modelled
bLocusLT671822:1,122,440–1,122,607undeterminedbE0fewer than 2 genes could be modelled
bLocusLT671822:1,244,210–1,244,515undeterminedbE0fewer than 2 genes could be modelled
bLocusLT671822:1,357,416–1,357,535undeterminedbE0fewer than 2 genes could be modelled
bLocusLT671825:142,758–142,910undeterminedbE0fewer than 2 genes could be modelled
bLocusLT671825:165,688–165,900undeterminedbE0fewer than 2 genes could be modelled
bLocusLT671825:231,113–231,211undeterminedbE0fewer than 2 genes could be modelled
bLocusLT671825:256,915–257,079undeterminedbE0fewer than 2 genes could be modelled
bLocusLT671825:375,327–375,467undeterminedbE0fewer than 2 genes could be modelled
bLocusLT671825:484,876–485,022undeterminedbE0fewer than 2 genes could be modelled
bLocusLT671825:590,274–590,465undeterminedbE0fewer than 2 genes could be modelled

Provenance

Genome file
MsympodialisATCC42132.genome.fasta
Assembly
9 contigs · 7.8 Mb · N50 1.4 Mb
Genome SHA-256
acf4b70ab65de8981243a47e42ed65c29e4d2aa1ed687bae2867bfc72f5b9ee7
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
2026-11-07T02:37:08Z
Run time
20 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