MATPredict · mating-type report

CdeneoformansJEC21

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 02:14 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 AE017344.1alpha locus: genes from left to right on AE017344.1, 1,518,721 to 1,640,752: PAN6 (conserved flank, minus strand); MFa (core MAT gene, minus strand); MFalpha (core MAT gene, minus strand); RPL39 (core MAT gene, plus strand); STE3 (core MAT gene, plus strand); SXI1 (core MAT gene, minus strand); FAO1 (conserved flank, minus strand).1,520 kb1,540 kb1,560 kb1,580 kb1,600 kb1,620 kb1,640 kb136.2 kb more to contig end →called locusPAN6: conserved flank, 1,518,721–1,520,388 (-), identity 100.0%, search hit onlyPAN6MFa: core MAT gene, 1,534,707–1,534,823 (-), identity 54.8%, search hit onlyMFa (lost to MFalpha)MFalpha: core MAT gene, 1,534,707–1,534,823 (-), identity 100.0%, search hit onlyMFalphaRPL39: core MAT gene, 1,540,410–1,540,908 (+), identity 100.0%, search hit onlyRPL39STE3: core MAT gene, 1,577,472–1,578,792 (+), identity 100.0%, search hit onlySTE3SXI1: core MAT gene, 1,637,262–1,638,622 (-), identity 100.0%, search hit onlySXI1FAO1: conserved flank, 1,639,391–1,640,752 (-), identity 100.0%, search hit onlyFAO1
Gene order on AE017344.1. Scroll sideways to see the whole figure.
FungiDB release 71 gene models on AE017344.1, 1,512,620 to 1,646,861CND05590 1,510,119-1,513,788 (+): autophagy-related proteinCND05590 APG9CND05600 1,514,502-1,515,040 (+): heat shock protein, 12KdaCND05600 HSP12CND05620 1,515,571-1,518,664 (+): hypothetical proteinCND05620CND05630 1,518,659-1,520,459 (-): pantoate-beta-alanine ligase, putativeCND05630 PAN6CND05640 1,520,576-1,523,650 (-): putative nucleolar gtp-binding proteinCND05640 NOG2CND05645 1,523,787-1,524,355 (+): hypothetical proteinCND05645CND05650 1,524,399-1,525,545 (-): mat3 pheromone repeat proteinCND05650 MAT3CND05660 1,525,690-1,528,817 (+): serine/threonine-protein kinaseCND05660 IKS1CND05670 1,529,562-1,533,533 (-): BTP/PZ domain-containing proteinCND05670 BSP3CND05680 1,534,507-1,535,072 (-): pheromone alphaCND05680 MFalpha2CND05690 1,535,299-1,535,805 (+): mating-type pheromone alphaCND05690 MFalpha3CND05700 1,540,279-1,541,624 (+): large subunit ribosomal protein L39CND05700 RPL39alphaCND05710 1,542,855-1,544,179 (+): hypothetical proteinCND05710CND05720 1,544,299-1,548,888 (+): PHD-finger | BAH domain | PHD-zinc-finger like domain | PHD-finger | domain-containing proteinCND05720CND05740 1,548,195-1,551,071 (-): RNA recognition motif | Eukaryotic translation initiation factor eIF2A | domain-containing proteinCND05740 PRT1CND05750 1,553,349-1,553,710 (+): pheromone alphaCND05750 MFalpha1CND05760 1,556,920-1,561,412 (-): mapkk kinase, ste/ste11 protein kinaseCND05760 STE11alphaCND05770 1,562,072-1,563,736 (-): electron transfer flavoprotein alpha subunitCND05770 ETF1alphaCND05780 1,564,625-1,570,904 (+): myosin class v heavy chainCND05780 MYO2alphaCND05790 1,571,061-1,574,076 (-): ste/ste20/paka protein kinaseCND05790 STE20alphaCND05800 1,577,361-1,578,873 (+): mating-type a-factor pheromone receptor, putativeCND05800 STE3alphaCND05810 1,579,482-1,583,736 (+): ste-like transcription factorCND05810 STE12alphaCND05820 1,584,694-1,589,127 (-): DNA-directed RNA polymeraseCND05820 RPO41alphaCND05830 1,589,282-1,592,251 (+): Armadillo/beta-catenin repeat proteinCND05830 BSP2CND05840 1,592,467-1,595,103 (-): putative dihydrolipoyl dehydrogenaseCND05840 LPD1alphaCND05850 1,595,246-1,598,617 (-): CID1-family polyA polymeraseCND05850 CID1alphaCND05860 1,599,025-1,602,637 (-): RhoGEF domain | domain-containing proteinCND05860CND05870 1,602,838-1,609,303 (-): phd transcription factorCND05870 RUM1alphaCND05880 1,609,560-1,611,001 (+): hypothetical proteinCND05880CND05890 1,610,973-1,612,545 (-): DDE superfamily endonuclease | domain-containing proteinCND05890CND05900 1,614,806-1,618,125 (+): protein of unknown functionCND05900 BSP1CND05910 1,620,941-1,621,957 (-): large subunit ribosomal protein L22eCND05910 RPL22alphaCND05920 1,623,333-1,629,716 (-): phospholipase D1CND05920 SPO14alphaCND05940 1,632,807-1,635,392 (+): capsular associated proteinCND05940 CAP1alphaCND05950 1,637,071-1,639,310 (-): sexual development regulatorCND05950 SXI1alphaCND05960 1,639,382-1,640,976 (-): putative fatty alcohol oxidase in the mating-type locusCND05960 FAO1CND05970 1,641,083-1,642,482 (+): cytosine deaminase, putativeCND05970CND05980 1,643,037-1,645,902 (+): uric acid xanthine permeaseCND05980 UAP1CND05990 1,646,200-1,649,366 (-): fungal Zn(2)-Cys(6) binuclear cluster domain-containing protein, putativeCND05990 HAP1
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
  • search hit only
Location
AE017344.1:1,518,721–1,640,752 · 122.0 kb
Own genes
AE017344.1:1,518,721–1,640,752 · 122.0 kb
Locus
Complete locus: MAT gene(s) with their flanking genes.
Genes modelled
6 of 7 gene hits
Nearest contig end
142.3 kb
Region (samtools)
AE017344.1:1518721-1640752
Idiomorph scores
  • alpha 762.0

Margin over the set-aside MFa hit: 45.2 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
MFalpha100.0MFa54.8100.0higher identity
MFalpha100.0MFa54.8100.0higher identity

Gene evidence

GeneRoleModel Identity %E-value Position (strand)Exons Reference recordFungiDB gene
PAN6conserved flankhit onlyDIAMOND, proteome100.0cov 100.0%5.7e-302806 bits1,518,721–1,520,388 -–40410_jec20_MAT_aCND05630 PAN6
MFacore MATlost to MFalpha, not countedhit onlyDIAMOND, proteome54.8cov 100.0%5.3e-0936 bits1,534,707–1,534,823 -–40410_jec20_MAT_aCND05680 MFalpha2
MFalphacore MAThit onlyDIAMOND, proteome100.0cov 100.0%5.3e-2474 bits1,534,707–1,534,823 -–40410_jec21_MAT_alphaCND05680 MFalpha2
RPL39core MAThit onlyDIAMOND, proteome100.0cov 100.0%2.1e-35103 bits1,540,410–1,540,908 +–40410_jec20_MAT_aCND05700 RPL39alpha
STE3core MAThit onlyDIAMOND, proteome100.0cov 100.0%5.4e-282753 bits1,577,472–1,578,792 +–40410_jec21_MAT_alphaCND05800 STE3alpha
SXI1core MAThit onlyDIAMOND, proteome100.0cov 100.0%1.2e-284762 bits1,637,262–1,638,622 -–40410_jec21_MAT_alphaCND05950 SXI1alpha
FAO1conserved flankhit onlyDIAMOND, proteome100.0cov 100.0%5.5e-263702 bits1,639,391–1,640,752 -–40410_jec21_MAT_alphaCND05960 FAO1
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
MATAE017342.1:1,238,923–1,240,383undeterminedSTE31too few of the family's genes found

Provenance

Genome file
CdeneoformansJEC21.genome.fasta
Assembly
14 contigs · 19.1 Mb · N50 1.4 Mb
Genome SHA-256
1ad38ae166c8c17b93013a1bfa0ecfab4ada9535223016aa89adcde3f02b09dc
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': 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
2026-11-07T02:14:20Z
Run time
27 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