MATPredict · mating-type report

HcapsulatumH88

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 02:32 UTC by MATPredict 0.8.1

Result

Mating type

MAT1-2medium confidence

Called loci 1

MAT1-2 MAT family · Ascomycota

medium confidence
Gene order of the MAT1-2 locus on CP069104MAT1-2 locus: genes from left to right on CP069104, 3,587,172 to 3,614,321: SLA2 (conserved flank, plus strand); CIMG_00407 (core MAT gene, minus strand); MAT1-2-4 (core MAT gene, minus strand); MAT1-1-3 (core MAT gene, plus strand); MAT1-2-1 (core MAT gene, plus strand); MAT1-1-4 (core MAT gene, minus strand); COX13 (conserved flank, minus strand); APN2 (conserved flank, plus strand); MAT1-1-1 (core MAT gene, plus strand).3,590 kb3,595 kb3,600 kb3,605 kb3,610 kb3,615 kb3,385.0 kb more to contig end →called locusSLA2: conserved flank, 3,587,172–3,591,464 (+), identity 90.7%, search hit onlySLA2CIMG_00407: core MAT gene, 3,593,701–3,594,306 (-), identity 40.0%, gene modelCIMG_00407MAT1-2-4: core MAT gene, 3,593,816–3,593,971 (-), identity 44.231%, search hit onlyMAT1-2-4MAT1-1-3: core MAT gene, 3,595,089–3,596,236 (+), identity 39.2%, search hit onlyMAT1-1-3 (lost to MAT1-2-1)MAT1-2-1: core MAT gene, 3,595,089–3,596,236 (+), identity 51.9%, search hit onlyMAT1-2-1MAT1-1-4: core MAT gene, 3,597,960–3,598,457 (-), identity 47.8%, gene modelMAT1-1-4COX13: conserved flank, 3,601,221–3,602,138 (-), identity 71.8%, search hit onlyCOX13APN2: conserved flank, 3,602,503–3,604,759 (+), identity 84.1%, search hit onlyAPN2MAT1-1-1: core MAT gene, 3,614,154–3,614,321 (+), identity 26.786%, search hit onlyMAT1-1-1
Gene order on CP069104. Scroll sideways to see the whole figure.
FungiDB release 71 gene models on CP069104, 3,585,815 to 3,615,677I7I53_01399 3,583,072-3,586,433 (+): putative PH domain-containing proteinI7I53_01399I7I53_01400 3,585,625-3,586,504 (-): hypothetical RNAI7I53_01400I7I53_01401 3,586,951-3,592,314 (+): cytoskeleton assembly control proteinI7I53_01401 SLA2I7I53_01402 3,591,484-3,593,083 (-): unspecified productI7I53_01402I7I53_01403 3,593,426-3,594,588 (-): unspecified productI7I53_01403I7I53_01404 3,594,733-3,596,436 (+): HMG box proteinI7I53_01404I7I53_01405 3,597,055-3,598,071 (-): unspecified productI7I53_01405I7I53_01406 3,598,209-3,598,938 (-): unspecified productI7I53_01406I7I53_01407 3,598,939-3,600,774 (-): hypothetical RNAI7I53_01407I7I53_01408 3,600,859-3,602,242 (-): cytochrome c oxidase subunit VIaI7I53_01408I7I53_01409 3,602,357-3,605,913 (+): DNA lyase Apn2I7I53_01409 APN2I7I53_01410 3,606,764-3,607,799 (+): unspecified productI7I53_01410I7I53_01411 3,607,909-3,613,010 (+): RNA polymerase II mediator complex component Srb8I7I53_01411 SRB8I7I53_01412 3,613,290-3,614,860 (+): complex I intermediate-associated protein CIA30I7I53_01412 CIA30I7I53_01413 3,614,729-3,616,167 (-): phosphoribosyl-aminoimidazole-succinocarboxamide synthaseI7I53_01413 ADE1
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
  • gene model
  • search hit only
Location
CP069104:3,587,172–3,614,321 · 27.1 kb
Own genes
CP069104:3,587,172–3,614,321 · 27.1 kb
Locus
Complete locus: MAT gene(s) with their flanking genes.
Genes modelled
6 of 9 gene hits
Nearest contig end
3.4 Mb
Region (samtools)
CP069104:3587172-3614321
Idiomorph scores
  • MAT1-2 296.0
  • MAT1-1 141.0

Margin over the next idiomorph: 155.0

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
MAT1-2-151.9MAT1-1-339.2100.0higher identity

Gene evidence

GeneRoleModel Identity %E-value Position (strand)Exons Reference recordFungiDB gene
SLA2conserved flankhit onlyDIAMOND, proteome90.7cov 99.3%< 1e-1801,581 bits3,587,172–3,591,464 +–107463_unknown-1_MAT_MAT1-2I7I53_01401 SLA2
CIMG_00407core MATgene modelexonerate40.0cov 62.4%1.1e-1577 bits3,593,701–3,594,306 -35501_rs_MAT_MAT1-2I7I53_01403
MAT1-2-4core MAThit onlytblastn44.2cov 21.0%2.9e-1052 bits3,593,816–3,593,971 -–746128_af293_MAT_MAT1-2I7I53_01403
MAT1-1-3core MATlost to MAT1-2-1, not countedhit onlyDIAMOND, proteome39.2cov 41.1%1.2e-1156 bits3,595,089–3,596,236 +–230073_uamh-1363_MAT_MAT1-1I7I53_01404
MAT1-2-1core MAThit onlyDIAMOND, proteome51.9cov 63.8%1.8e-101296 bits3,595,089–3,596,236 +–162425_fgsc-a4_MAT_combinedI7I53_01404
MAT1-1-4core MATgene modelexonerate47.8cov 67.5%5.2e-38141 bits3,597,960–3,598,457 -1199306_rmscc1040_MAT_MAT1-1I7I53_01405
I7I53_01406
COX13conserved flankhit onlyDIAMOND, proteome71.8cov 100.0%3.9e-60175 bits3,601,221–3,602,138 -–199306_rmscc1040_MAT_MAT1-1I7I53_01408
APN2conserved flankhit onlyDIAMOND, proteome84.1cov 36.7%4.5e-256712 bits3,602,503–3,604,759 +–2903220_liq80xsp_MAT_combinedI7I53_01409 APN2
MAT1-1-1core MAThit onlytblastn26.8cov 16.0%5.1e+0029 bits3,614,154–3,614,321 +–5518_3639_MAT_combinedI7I53_01412 CIA30

Withheld candidate loci 1

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: too few of the family's genes found (1).

Show the 1 withheld locus

Withheld loci (1)

familylocationidiomorph genesmodelledreason
MATCP069102:3,546,116–3,548,458MAT1-2MAT1-2-11too few of the family's genes found

Provenance

Genome file
HcapsulatumH88.genome.fasta
Assembly
7 contigs · 38.0 Mb · N50 7.0 Mb
Genome SHA-256
3478008605131bd449e375c0152298cfa318a4ed407258b82444ae23c583c46f
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': 299071, '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': 1, 'genetic_code_from': 'family taxid 299071', 'routed_by': 'family taxid 299071 (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, scoped_roster=off: BGL1,GAP1 not searched, supported_min_bitscore=33.0
Run started
2026-11-07T02:31:30Z
Run time
78 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