MATPredict · mating-type report

CneoformansH99

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

alphahigh confidence

Called loci 1

alpha MAT family · Basidiomycota

high confidence
Gene order of the alpha locus on CP003824.1alpha locus: genes from left to right on CP003824.1, 183,859 to 286,720: FAO1 (conserved flank, plus strand); SXI1 (core MAT gene, plus strand); STE3 (core MAT gene, minus strand); MFa (core MAT gene, minus strand); MFalpha (core MAT gene, plus strand); RPL39 (core MAT gene, plus strand); PAN6 (conserved flank, plus strand).180 kb200 kb220 kb240 kb260 kb280 kb← 178.7 kb more to contig endcalled locusFAO1: conserved flank, 183,859–185,218 (+), identity 94.4%, search hit onlyFAO1SXI1: core MAT gene, 185,988–187,349 (+), identity 80.7%, search hit onlySXI1STE3: core MAT gene, 208,374–209,695 (-), identity 94.5%, search hit onlySTE3MFa: core MAT gene, 222,503–222,616 (-), identity 52.381%, search hit onlyMFa (lost to MFalpha)MFalpha: core MAT gene, 222,931–223,047 (+), identity 86.8%, search hit onlyMFalphaRPL39: core MAT gene, 270,550–271,048 (+), identity 100.0%, search hit onlyRPL39PAN6: conserved flank, 284,943–286,720 (+), identity 92.0%, search hit onlyPAN6
Gene order on CP003824.1. Scroll sideways to see the whole figure.
FungiDB release 68 gene models on CP003824.1, 178,711 to 291,866CNAG_06818 175,237-178,834 (+): Putative Zn(II)2Cys6 transcription factorCNAG_06818 HAP1CNAG_06817 178,722-181,616 (-): uric acid xanthine permeaseCNAG_06817 UAP1CNAG_06816 182,119-185,466 (-): hypothetical proteinCNAG_06816CNAG_12420 182,123-183,182 (+): unspecified productCNAG_12420CNAG_06815 183,564-185,652 (+): putative fatty alcohol oxidaseCNAG_06815 FAO1CNAG_06814 185,700-188,859 (+): Alpha cell-type homeodomain transcription factorCNAG_06814 SXI1alphaCNAG_12421 185,870-187,569 (-): unspecified productCNAG_12421CNAG_12422 189,214-189,533 (+): unspecified productCNAG_12422CNAG_06813 189,560-192,241 (-): O-glucosyltransferase, putativeCNAG_06813 CAP1alphaCNAG_12423 192,372-192,704 (-): unspecified productCNAG_12423CNAG_12424 192,935-194,380 (+): unspecified productCNAG_12424CNAG_06812 193,324-200,779 (-): phospholipase D, variantCNAG_06812 SPO14alphaCNAG_06811 200,909-202,001 (+): large subunit ribosomal protein L22eCNAG_06811 RPL22alphaCNAG_06810 202,602-204,039 (+): hypothetical proteinCNAG_06810CNAG_06809 204,044-207,447 (-): IKS protein kinaseCNAG_06809 IKS1CNAG_12425 207,817-208,498 (+): unspecified productCNAG_12425CNAG_06808 208,236-209,840 (-): pheromone a factor receptorCNAG_06808 STE3alphaCNAG_06807 210,557-211,580 (-): hypothetical proteinCNAG_06807CNAG_06806 212,068-213,909 (+): electron transfer flavoprotein alpha subunitCNAG_06806 ETF1alphaCNAG_12426 214,174-214,705 (-): unspecified productCNAG_12426CNAG_06805 214,530-215,070 (+): hypothetical proteinCNAG_06805CNAG_06804 215,850-219,594 (-): BTP/PZ domain-containing proteinCNAG_06804 BSP3CNAG_07406 222,288-222,701 (-): pheromone alphaCNAG_07406CNAG_07407 222,704-223,314 (+): fungal mating-type pheromoneCNAG_07407 MFalpha3CNAG_12427 223,329-223,829 (+): unspecified productCNAG_12427CNAG_06971 223,846-230,310 (+): myosin class v heavy chainCNAG_06971 MYO2alphaCNAG_07408 230,211-233,167 (-): STE/STE20/PAKA protein kinase, variantCNAG_07408 STE20alphaCNAG_06980 233,496-238,299 (+): STE/STE11 protein kinaseCNAG_06980 STE11alphaCNAG_07409 238,263-242,729 (-): DNA-directed RNA polymerase, mitochondrialCNAG_07409 RPO41alphaCNAG_07005 242,901-246,213 (+): Armadillo/beta-catenin repeat proteinCNAG_07005 BSP2CNAG_07004 244,073-247,927 (-): dihydrolipoyl dehydrogenaseCNAG_07004 LPD1alphaCNAG_07410 248,015-251,440 (-): CID1-family polyA polymeraseCNAG_07410 CID1alphaCNAG_07015 251,935-255,597 (-): hypothetical proteinCNAG_07015CNAG_07411 256,515-263,236 (+): histone demethylase JARID1CNAG_07411 RUM1alphaCNAG_01457 263,567-266,561 (+): hypothetical proteinCNAG_01457 BSP1CNAG_01456 267,859-269,211 (+): hypothetical protein, variantCNAG_01456CNAG_12428 269,260-270,268 (-): unspecified productCNAG_12428CNAG_01455 270,518-271,941 (+): large subunit ribosomal protein L39CNAG_01455 RPL39alphaCNAG_01454 271,944-275,730 (-): transcription factor STE12CNAG_01454 STE12alphaCNAG_12429 276,399-277,159 (+): unspecified productCNAG_12429CNAG_07412 277,218-277,511 (-): hypothetical proteinCNAG_07412CNAG_01452 280,007-281,233 (+): mat3 pheromone repeat proteinCNAG_01452 MAT3CNAG_01451 280,948-281,513 (-): hypothetical proteinCNAG_01451CNAG_07413 281,653-284,758 (+): nucleolar GTP-binding protein 2CNAG_07413 NOG2CNAG_07414 284,872-286,790 (+): pantoate-beta-alanine ligaseCNAG_07414 PAN6CNAG_01448 286,747-290,119 (-): hypothetical proteinCNAG_01448CNAG_01446 290,468-291,329 (-): heat shock protein, 12KdaCNAG_01446 HSP12CNAG_01445 291,364-295,513 (-): autophagy-like protein 9CNAG_01445 APG9
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
  • conserved flank
  • search hit only
Location
CP003824.1:183,859–286,720 · 102.9 kb
Own genes
CP003824.1:183,859–286,720 · 102.9 kb
Locus
Complete locus: MAT gene(s) with their flanking genes.
Genes modelled
6 of 7 gene hits
Nearest contig end
183.9 kb
Region (samtools)
CP003824.1:183859-286720
Idiomorph scores
  • alpha 619.0
  • a 27.3

Margin over the next idiomorph: 591.7

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
MFalpha86.8MFa52.4100.0higher identity

Gene evidence

GeneRoleModel Identity %E-value Position (strand)Exons Reference recordFungiDB gene
FAO1conserved flankhit onlyDIAMOND, proteome94.4cov 100.0%3.4e-248664 bits183,859–185,218 +–40410_jec20_MAT_aCNAG_06816 (opposite strand)
CNAG_06815 FAO1
SXI1core MAThit onlyDIAMOND, proteome80.7cov 100.0%7.8e-228619 bits185,988–187,349 +–40410_jec21_MAT_alphaCNAG_06814 SXI1alpha
CNAG_12421 (opposite strand)
STE3core MAThit onlyDIAMOND, proteome94.5cov 100.0%9.1e-265710 bits208,374–209,695 -–40410_jec21_MAT_alphaCNAG_12425 (opposite strand)
CNAG_06808 STE3alpha
MFacore MATlost to MFalpha, not countedhit onlytblastn52.4cov 100.0%1.1e-0127 bits222,503–222,616 -–40410_jec20_MAT_aCNAG_07406
MFalphacore MAThit onlyDIAMOND, proteome86.8cov 100.0%4.2e-2167 bits222,931–223,047 +–40410_jec21_MAT_alphaCNAG_07407 MFalpha3
RPL39core MAThit onlyDIAMOND, proteome100.0cov 100.0%2.1e-35103 bits270,550–271,048 +–40410_jec20_MAT_aCNAG_01455 RPL39alpha
PAN6conserved flankhit onlyDIAMOND, proteome92.0cov 100.0%2.4e-274737 bits284,943–286,720 +–40410_jec20_MAT_aCNAG_07414 PAN6
NOG2not searchable: no reference protein in the database–
UAP1not searchable: no reference protein in the database–

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
MATCP003821.1:1,226,370–1,227,826undeterminedSTE31too few of the family's genes found

Provenance

Genome file
CneoformansH99.genome.fasta
Assembly
15 contigs · 18.9 Mb · N50 1.4 Mb
Genome SHA-256
022753e13883b4b3a92b934a4b31e0922ecb9ec32ff07476eb9f4d3ffe686a5a
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': 'genus', 'routing_taxid': 1884633, '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 1884633', 'routed_by': 'family taxid 1884633 (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
2026-11-07T01:57:10Z
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