MATPredict · mating-type report

CtropicalisMYA3404-2020

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 02:17 UTC by MATPredict 0.8.1

Result

Mating type

alphahigh confidence

Called loci 1

alpha MTL family · Ascomycota

high confidence
Gene order of the alpha locus on CP047873alpha locus: genes from left to right on CP047873, 1,047,566 to 1,056,179: MTLalpha2 (core MAT gene, minus strand); MTLA1 (core MAT gene, minus strand); OBP1 (variable flank, plus strand); PIK1 (variable flank, plus strand); MTLalpha1 (core MAT gene, plus strand); PAP1 (variable flank, minus strand).1,048 kb1,050 kb1,052 kb1,054 kb1,056 kb183.1 kb more to contig end →called locusMTLalpha2: core MAT gene, 1,047,566–1,048,180 (-), identity 46.3%, search hit onlyMTLalpha2MTLA1: core MAT gene, 1,047,686–1,047,805 (-), identity 37.5%, search hit onlyMTLA1 (lost to MTLalpha2)OBP1: variable flank, 1,049,086–1,050,372 (+), identity 82.8%, search hit onlyOBP1PIK1: variable flank, 1,050,632–1,053,550 (+), identity 70.0%, search hit onlyPIK1MTLalpha1: core MAT gene, 1,053,879–1,054,457 (+), identity 61.5%, search hit onlyMTLalpha1PAP1: variable flank, 1,054,506–1,056,179 (-), identity 81.5%, search hit onlyPAP1
Gene order on CP047873. Scroll sideways to see the whole figure.
FungiDB release 71 gene models on CP047873, 1,047,135 to 1,056,609CTMYA2_056780 1,047,566-1,048,180 (-): Homeobox KN domain | domain-containing proteinCTMYA2_056780CTMYA2_056790 1,049,086-1,050,372 (+): Oxysterol-binding protein | domain-containing proteinCTMYA2_056790CTMYA2_056800 1,050,632-1,053,550 (+): Phosphoinositide 3-kinase family, accessory domain (PIK domain) | Yeast phosphatidylinositol-4-OH kinase Pik1 | Phosphatidylinositol 3- and 4-kinase | domain-containing proteinCTMYA2_056800CTMYA2_056810 1,053,879-1,054,457 (+): Mating-type protein MAT alpha 1 HMG-box | domain-containing proteinCTMYA2_056810CTMYA2_056820 1,054,506-1,056,179 (-): Poly(A) polymerase nucleotidyltransferase domain | Poly(A) polymerase predicted RNA binding domain | Poly(A) polymerase central domain | domain-containing proteinCTMYA2_056820
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
  • variable flank
  • search hit only
  • MTLA1 is a weak hit to the other idiomorph's gene and was not counted against the call.
Location
CP047873:1,047,566–1,056,179 · 8.6 kb
Cross-lineage class
MAT1-1
Own genes
CP047873:1,047,566–1,056,179 · 8.6 kb
Locus
Complete locus: MAT gene(s) with their flanking genes.
Genes modelled
5 of 6 gene hits
Nearest contig end
183.5 kb
Region (samtools)
CP047873:1047566-1056179
Idiomorph scores
  • alpha 231.0

Margin over the set-aside MTLA1 hit: 8.8 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
MTLalpha246.3MTLA137.5100.0higher identity

Gene evidence

GeneRoleModel Identity %E-value Position (strand)Exons Reference recordFungiDB gene
MTLalpha2core MAThit onlyDIAMOND, proteome46.3cov 98.4%7.6e-50152 bits1,047,566–1,048,180 -–42374_d1558_MTL_alphaCTMYA2_056780
MTLA1core MATother idiomorph, not countedlost to MTLalpha2, not countedhit onlytblastn37.5cov 22.0%9.4e-0128 bits1,047,686–1,047,805 -–498019_b11243_MTL_ACTMYA2_056780
OBP1variable flankhit onlyDIAMOND, proteome82.8cov 100.0%3.5e-266719 bits1,049,086–1,050,372 +–5476_sc5314_MTL_alphaCTMYA2_056790
PIK1variable flankhit onlyDIAMOND, proteome70.0cov 99.3%< 1e-1801,290 bits1,050,632–1,053,550 +–5476_sc5314_MTL_alphaCTMYA2_056800
MTLalpha1core MAThit onlyDIAMOND, proteome61.5cov 99.5%5.1e-81231 bits1,053,879–1,054,457 +–42374_d1558_MTL_alphaCTMYA2_056810
PAP1variable flankhit onlyDIAMOND, proteome81.5cov 99.8%< 1e-180922 bits1,054,506–1,056,179 -–5476_sc5314_MTL_alphaCTMYA2_056820

Withheld candidate loci 34

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 (31); too few of the family's genes found (3).

Show the 34 withheld loci

Withheld loci (34)

familylocationidiomorph genesmodelledreason
MTLCP047869:531,483–531,581alphaMTLalpha10fewer than 2 genes could be modelled
MTLCP047869:768,712–768,915AMTLA20fewer than 2 genes could be modelled
MTLCP047869:1,271,808–1,293,181alphaMTLalpha10fewer than 2 genes could be modelled
MTLCP047869:1,587,889–1,588,080alphaMTLalpha10fewer than 2 genes could be modelled
MTLCP047869:1,898,812–1,919,556AMTLA10fewer than 2 genes could be modelled
MTLCP047870:412,989–413,102AMTLA20fewer than 2 genes could be modelled
MTLCP047870:469,385–469,495alphaMTLalpha10fewer than 2 genes could be modelled
MTLCP047870:887,524–887,664alphaMTLalpha10fewer than 2 genes could be modelled
MTLCP047870:1,413,159–1,413,338AMTLA20fewer than 2 genes could be modelled
MTLCP047870:2,364,071–2,364,214AMTLA10fewer than 2 genes could be modelled
MTLCP047870:2,434,716–2,434,838AMTLA10fewer than 2 genes could be modelled
MTLCP047873:71,830–71,997AMTLA10fewer than 2 genes could be modelled
MTLCP047873:543,485–543,625alphaMTLalpha10fewer than 2 genes could be modelled
MTLCP047873:645,965–646,108alphaMTLalpha10fewer than 2 genes could be modelled
MTLCP047873:1,099,549–1,099,689AMTLA10fewer than 2 genes could be modelled
MTLCP047873:1,148,781–1,148,984AMTLA20fewer than 2 genes could be modelled
MTLCP047873:1,174,066–1,174,389AMTLA20fewer than 2 genes could be modelled
MTLCP047875:583,224–583,343AMTLA20fewer than 2 genes could be modelled
MTLCP047875:891,504–891,626alphaMTLalpha10fewer than 2 genes could be modelled
MTLCP047875:1,178,470–1,178,598AMTLA20fewer than 2 genes could be modelled
MTLCP047875:1,437,563–1,437,835AMTLA10fewer than 2 genes could be modelled
MTLCP047875:1,563,493–1,563,606AMTLA20fewer than 2 genes could be modelled
MTLCP047875:2,032,340–2,053,302AMTLA1, MTLA20fewer than 2 genes could be modelled
MTLCP047874:660,786–661,058AMTLA20fewer than 2 genes could be modelled
MTLCP047874:826,470–839,824AMTLA1, MTLalpha10fewer than 2 genes could be modelled
MTLCP047871:788,001–788,147AMTLA10fewer than 2 genes could be modelled
MTLCP047871:1,771,187–1,771,288AMTLA10fewer than 2 genes could be modelled
MTLCP047872:197,497–197,586AMTLA10fewer than 2 genes could be modelled
MTLCP047872:562,707–562,895alphaMTLalpha10fewer than 2 genes could be modelled
MTLCP047872:1,376,144–1,376,245alphaMTLalpha10fewer than 2 genes could be modelled
MTLCP047872:1,478,225–1,478,365AMTLA20fewer than 2 genes could be modelled
MTLCP047869:1,814,193–1,815,473undeterminedOBP11too few of the family's genes found
MTLCP047870:1,221,493–1,224,531undeterminedPIK11too few of the family's genes found
MTLCP047875:617,617–623,361undeterminedPIK11too few of the family's genes found

Provenance

Genome file
CtropicalisMYA3404-2020.genome.fasta
Assembly
7 contigs · 14.6 Mb · N50 2.5 Mb
Genome SHA-256
fca794d6c7c909792222d666b8561df6f15b1cce88c52a31435e035f96eabcad
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': 'genus', 'routing_taxid': 766764, '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 Ascomycota', 'action': 'routed', 'weak_call_accepted': False, 'genetic_code': 12, 'genetic_code_from': 'family taxid 766764', 'routed_by': 'family taxid 766764 (lineage)'}, genetic_code=12, 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
2026-11-07T02:17:16Z
Run time
24 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