MATPredict · mating-type report

CtropicalisMYA3404

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 01:57 UTC by MATPredict 0.8.1

Result

Mating-type loci

alphahigh confidenceAhigh confidence

Called loci 2

alpha MTL family · Ascomycota

high confidence
Gene order of the alpha locus on GG692402alpha locus: genes from left to right on GG692402, 177,475 to 186,091: PAP1 (variable flank, plus strand); MTLalpha1 (core MAT gene, minus strand); PIK1 (variable flank, minus strand); OBP1 (variable flank, minus strand); MTLalpha2 (core MAT gene, plus strand); MTLA1 (core MAT gene, plus strand).178 kb180 kb182 kb184 kb186 kb← 177.0 kb more to contig endcalled locusPAP1: variable flank, 177,475–179,151 (+), identity 81.5%, search hit onlyPAP1MTLalpha1: core MAT gene, 179,194–179,775 (-), identity 61.5%, search hit onlyMTLalpha1PIK1: variable flank, 180,101–183,022 (-), identity 70.0%, search hit onlyPIK1OBP1: variable flank, 183,279–184,568 (-), identity 82.8%, search hit onlyOBP1MTLalpha2: core MAT gene, 185,474–186,091 (+), identity 46.3%, search hit onlyMTLalpha2MTLA1: core MAT gene, 185,849–185,968 (+), identity 37.5%, search hit onlyMTLA1 (lost to MTLalpha2)
Gene order on GG692402. Scroll sideways to see the whole figure.
FungiDB release 68 gene models on GG692402, 177,045 to 186,521CTRG_05298 177,475-179,151 (+): Poly(A) polymerase PAPalphaCTRG_05298CTRG_05299 179,194-179,775 (-): hypothetical proteinCTRG_05299CTRG_05300 180,101-183,022 (-): phosphatidylinositol 4-kinase PIK1alphaCTRG_05300CTRG_05301 183,279-184,568 (-): hypothetical proteinCTRG_05301CTRG_05302 185,474-186,091 (+): hypothetical proteinCTRG_05302
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
  • variable flank
  • search hit only
  • MTLA1 is a weak hit to the other idiomorph's gene and was not counted against the call.
Location
GG692402:177,475–186,091 · 8.6 kb
Cross-lineage class
MAT1-1
Own genes
GG692402:177,475–186,091 · 8.6 kb
Locus
Complete locus: MAT gene(s) with their flanking genes.
Genes modelled
5 of 6 gene hits
Nearest contig end
177.5 kb
Region (samtools)
GG692402:177475-186091
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
PAP1variable flankhit onlyDIAMOND, proteome81.5cov 99.8%< 1e-180922 bits177,475–179,151 +–5476_sc5314_MTL_alphaCTRG_05298
MTLalpha1core MAThit onlyDIAMOND, proteome61.5cov 99.5%5.1e-81231 bits179,194–179,775 -–42374_d1558_MTL_alphaCTRG_05299
PIK1variable flankhit onlyDIAMOND, proteome70.0cov 99.3%< 1e-1801,290 bits180,101–183,022 -–5476_sc5314_MTL_alphaCTRG_05300
OBP1variable flankhit onlyDIAMOND, proteome82.8cov 100.0%3.5e-266719 bits183,279–184,568 -–5476_sc5314_MTL_alphaCTRG_05301
MTLalpha2core MAThit onlyDIAMOND, proteome46.3cov 98.4%7.6e-50152 bits185,474–186,091 +–42374_d1558_MTL_alphaCTRG_05302
MTLA1core MATother idiomorph, not countedlost to MTLalpha2, not countedhit onlytblastn37.5cov 22.0%9.5e-0128 bits185,849–185,968 +–498019_b11243_MTL_ACTRG_05302

A MTL family · Ascomycota

high confidence
Gene order of the A locus on GG692408A locus: genes from left to right on GG692408, 754 to 8,933: PAP1 (variable flank, minus strand); OBP1 (variable flank, plus strand); PIK1 (variable flank, plus strand); MTLA2 (core MAT gene, plus strand); MTLA1 (core MAT gene, plus strand).2 kb4 kb6 kb8 kbcontig endcalled locusPAP1: variable flank, 754–2,427 (-), identity 82.9%, search hit onlyPAP1OBP1: variable flank, 2,826–4,106 (+), identity 81.8%, search hit onlyOBP1PIK1: variable flank, 4,383–7,229 (+), identity 73.3%, search hit onlyPIK1MTLA2: core MAT gene, 7,360–8,021 (+), identity 50.0%, gene modelMTLA2MTLA1: core MAT gene, 8,487–8,933 (+), identity 55.1%, search hit onlyMTLA1
Gene order on GG692408. Scroll sideways to see the whole figure.
FungiDB release 68 gene models on GG692408, 1 to 9,341CTRG_06235 12-395 (+): predicted proteinCTRG_06235CTRG_06236 754-2,427 (-): Poly(A) polymerase PAPaCTRG_06236CTRG_06237 2,826-4,106 (+): hypothetical proteinCTRG_06237CTRG_06238 4,383-7,229 (+): phosphatidylinositol 4-kinase PIK1aCTRG_06238CTRG_06239 8,487-8,933 (+): hypothetical proteinCTRG_06239CTRG_06240 9,143-11,329 (-): predicted proteinCTRG_06240
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
  • variable flank
  • gene model
  • search hit only
Location
GG692408:754–8,933 · 8.2 kb
Cross-lineage class
MAT1-2
Own genes
GG692408:754–8,933 · 8.2 kb
Locus
Complete locus: MAT gene(s) with their flanking genes.
Genes modelled
5 of 5 gene hits
Nearest contig end
753 bp
Region (samtools)
GG692408:754-8933
Idiomorph scores
  • A 111.0

No other idiomorph scored.

Score: bitscore of the best core-gene hit for each idiomorph.

Gene evidence

GeneRoleModel Identity %E-value Position (strand)Exons Reference recordFungiDB gene
PAP1variable flankhit onlyDIAMOND, proteome82.9cov 100.0%< 1e-180934 bits754–2,427 -–5476_sc5314_MTL_ACTRG_06236
OBP1variable flankhit onlyDIAMOND, proteome81.8cov 100.0%3.6e-266719 bits2,826–4,106 +–5476_sc5314_MTL_ACTRG_06237
PIK1variable flankhit onlyDIAMOND, proteome73.3cov 99.5%< 1e-1801,320 bits4,383–7,229 +–5476_sc5314_MTL_ACTRG_06238
MTLA2core MATgene modelexonerate50.0cov 100.0%8.6e-39102 bits7,360–8,021 +25476_sc5314_MTL_Anone
MTLA1core MAThit onlyDIAMOND, proteome55.1cov 54.3%3.7e-34111 bits8,487–8,933 +–5476_sc5314_MTL_ACTRG_06239

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 (32); too few of the family's genes found (2).

Show the 34 withheld loci

Withheld loci (34)

familylocationidiomorph genesmodelledreason
MTLGG692396:913,014–933,762AMTLA10fewer than 2 genes could be modelled
MTLGG692396:1,232,886–1,233,077alphaMTLalpha10fewer than 2 genes could be modelled
MTLGG692396:1,527,816–1,549,192alphaMTLalpha10fewer than 2 genes could be modelled
MTLGG692396:2,050,682–2,050,885AMTLA20fewer than 2 genes could be modelled
MTLGG692396:2,272,477–2,272,575alphaMTLalpha10fewer than 2 genes could be modelled
MTLGG692398:146,341–146,460AMTLA20fewer than 2 genes could be modelled
MTLGG692398:454,648–454,770alphaMTLalpha10fewer than 2 genes could be modelled
MTLGG692398:741,647–741,775AMTLA20fewer than 2 genes could be modelled
MTLGG692398:998,011–998,283AMTLA10fewer than 2 genes could be modelled
MTLGG692398:1,124,018–1,124,131AMTLA20fewer than 2 genes could be modelled
MTLGG692398:1,592,415–1,613,377AMTLA1, MTLA20fewer than 2 genes could be modelled
MTLGG692399:406,876–406,989AMTLA20fewer than 2 genes could be modelled
MTLGG692399:463,235–463,345alphaMTLalpha10fewer than 2 genes could be modelled
MTLGG692399:881,120–881,260alphaMTLalpha10fewer than 2 genes could be modelled
MTLGG692399:1,215,070–1,220,103AMTLA1, PIK11fewer than 2 genes could be modelled
MTLGG692402:60,591–84,845AMTLA20fewer than 2 genes could be modelled
MTLGG692402:133,964–134,104AMTLA10fewer than 2 genes could be modelled
MTLGG692402:587,582–587,725alphaMTLalpha10fewer than 2 genes could be modelled
MTLGG692402:690,073–690,213alphaMTLalpha10fewer than 2 genes could be modelled
MTLGG692405:354,594–354,761AMTLA10fewer than 2 genes could be modelled
MTLGG692407:19,039–19,164AMTLA10fewer than 2 genes could be modelled
MTLGG692400:220,346–220,468AMTLA10fewer than 2 genes could be modelled
MTLGG692400:290,976–291,119AMTLA10fewer than 2 genes could be modelled
MTLGG692400:1,241,866–1,242,045AMTLA20fewer than 2 genes could be modelled
MTLGG692401:85,368–98,716AMTLA1, MTLalpha10fewer than 2 genes could be modelled
MTLGG692401:264,779–265,051AMTLA20fewer than 2 genes could be modelled
MTLGG692395:781,128–781,274AMTLA10fewer than 2 genes could be modelled
MTLGG692395:1,763,748–1,763,849AMTLA10fewer than 2 genes could be modelled
MTLGG692397:741,777–741,917AMTLA20fewer than 2 genes could be modelled
MTLGG692397:843,904–844,005alphaMTLalpha10fewer than 2 genes could be modelled
MTLGG692397:1,655,462–1,655,650alphaMTLalpha10fewer than 2 genes could be modelled
MTLGG692397:2,022,012–2,022,101AMTLA10fewer than 2 genes could be modelled
MTLGG692396:1,017,117–1,018,400undeterminedOBP11too few of the family's genes found
MTLGG692398:180,734–186,481undeterminedPIK11too few of the family's genes found

Provenance

Genome file
CtropicalisMYA3404.genome.fasta
Assembly
24 contigs · 14.6 Mb · N50 1.7 Mb
Genome SHA-256
9b21d368bc801f8ef0710ea682ee6835906bf6567912a005a9ed5a77ab1ad637
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
2026-11-07T01:56:42Z
Run time
23 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