MATPredict · mating-type report

CdeneoformansB-3501A

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 CM000043alpha locus: genes from left to right on CM000043, 145,754 to 267,812: 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, minus strand); RPL39 (core MAT gene, minus strand); PAN6 (conserved flank, plus strand).140 kb160 kb180 kb200 kb220 kb240 kb260 kb← 139.7 kb more to contig endcalled locusFAO1: conserved flank, 145,754–147,115 (+), identity 100.0%, search hit onlyFAO1SXI1: core MAT gene, 147,884–149,244 (+), identity 100.0%, search hit onlySXI1STE3: core MAT gene, 207,712–209,032 (-), identity 100.0%, search hit onlySTE3MFa: core MAT gene, 232,996–233,109 (-), identity 54.762%, search hit onlyMFa (lost to MFalpha)MFalpha: core MAT gene, 232,996–233,109 (-), identity 100.0%, gene modelMFalphaRPL39: core MAT gene, 245,597–245,876 (-), identity 100.0%, search hit onlyRPL39PAN6: conserved flank, 266,145–267,812 (+), identity 100.0%, search hit onlyPAN6
Gene order on CM000043. Scroll sideways to see the whole figure.
FungiDB release 71 gene models on CM000043, 139,658 to 273,916CNBD0410 137,228-140,145 (+): Zn2-Cys6 transcription factorCNBD0410 HAP1CNBD0420 140,888-143,071 (-): uric acid xanthine permeaseCNBD0420 UAP1CNBD0430 144,122-145,191 (-): Cytidine and deoxycytidylate deaminase zinc-binding region | domain-containing proteinCNBD0430CNBD0440 145,754-147,115 (+): putative fatty alcohol oxidase in the mating-type locusCNBD0440 FAO1CNBD0450 147,884-149,244 (+): alpha cell-type homeodomain transcription factorCNBD0450 SXI1alphaCNBD0460 151,378-153,630 (-): O-glucosyltransferaseCNBD0460 CAP1alphaCNBD0470 157,490-162,969 (+): phospholipase D1CNBD0470 SPO14alphaCNBD0480 164,632-165,246 (+): large subunit ribosomal protein L22eCNBD0480 RPL22alphaCNBD0490 168,821-171,584 (-): Structure-specific endonuclease subunit SLX4CNBD0490 BSP1CNBD0500 174,072-175,467 (+): DDE superfamily endonuclease | domain-containing proteinCNBD0500CNBD0510 175,533-176,854 (-): unspecified productCNBD0510CNBD0520 177,362-183,348 (+): phd transcription factorCNBD0520 RUM1alphaCNBD0530 184,229-187,367 (+): RhoGEF domain | domain-containing proteinCNBD0530CNBD0540 188,203-191,124 (+): cid1-family polyA polymeraseCNBD0540 CID1alphaCNBD0550 191,479-193,553 (+): putative dihydrolipoyl dehydrogenaseCNBD0550 LPD1alphaCNBD0560 194,445-197,164 (-): armadillo/beta-catenin repeat protein, encoded on mat locusCNBD0560 BSP2CNBD0570 197,757-201,763 (+): DNA-directed mRNA polymerase, mitochondrialCNBD0570 RPO41alphaCNBD0580 203,217-206,414 (-): ste-like transcription factorCNBD0580 STE12alphaCNBD0590 207,712-209,032 (-): a-factor pheromone receptorCNBD0590 STE3alphaCNBD0600 212,727-215,143 (+): ste/ste20/paka protein kinaseCNBD0600 STE20alphaCNBD0610 215,699-221,542 (-): myosin class v heavy chainCNBD0610 MYO2alphaCNBD0620 222,834-224,249 (+): electron transfer flavoprotein alpha subunitCNBD0620 ETF1alphaCNBD0630 225,422-229,418 (+): mapkk kinase, ste/ste11 protein kinaseCNBD0630 STE11alphaCNBD0640 235,485-238,145 (+): RNA recognition motif | Eukaryotic translation initiation factor eIF2A | domain-containing proteinCNBD0640 PRT1CNBD0650 238,273-240,269 (-): PHD-zinc-finger like domain | PHD-finger | domain-containing proteinCNBD0650CNBD0660 240,720-241,944 (-): BAH domain | PHD-finger | domain-containing proteinCNBD0660CNBD0670 242,437-243,642 (-): unspecified productCNBD0670CNBD0680 245,597-245,876 (-): large subunit ribosomal protein L39CNBD0680 RPL39alphaCNBD0690 253,729-256,582 (+): btp/pz domain proteinCNBD0690 BSP3CNBD0700 257,949-260,636 (-): serine/threonine-protein kinaseCNBD0700 IKS1CNBD0710 260,976-261,888 (+): mat3 pheromone repeat proteinCNBD0710 MAT3CNBD0720 262,882-265,794 (+): putative nucleolar gtp-binding proteinCNBD0720 NOG2CNBD0730 266,145-267,812 (+): pantoate-beta-alanine ligaseCNBD0730 PAN6CNBD0740 268,021-270,646 (-): unspecified productCNBD0740CNBD0750 270,999-271,346 (-): unspecified productCNBD0750CNBD0760 271,563-271,925 (-): heat shock protein, 12KdaCNBD0760 HSP12CNBD0770 272,654-275,885 (-): autophagy-related proteinCNBD0770 APG9
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
CM000043:145,754–267,812 · 122.1 kb
Own genes
CM000043:145,754–267,812 · 122.1 kb
Locus
Complete locus: MAT gene(s) with their flanking genes.
Genes modelled
6 of 7 gene hits
Nearest contig end
145.8 kb
Region (samtools)
CM000043:145754-267812
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
MFalpha100.0MFa54.8100.0higher identity

Gene evidence

GeneRoleModel Identity %E-value Position (strand)Exons Reference recordFungiDB gene
FAO1conserved flankhit onlyDIAMOND, proteome100.0cov 100.0%5.5e-263702 bits145,754–147,115 +–40410_jec21_MAT_alphaCNBD0440 FAO1
SXI1core MAThit onlyDIAMOND, proteome100.0cov 100.0%1.2e-284762 bits147,884–149,244 +–40410_jec21_MAT_alphaCNBD0450 SXI1alpha
STE3core MAThit onlyDIAMOND, proteome100.0cov 100.0%5.4e-282753 bits207,712–209,032 -–40410_jec21_MAT_alphaCNBD0590 STE3alpha
MFacore MATlost to MFalpha, not countedhit onlytblastn54.8cov 100.0%5.0e-0742 bits232,996–233,109 -–40410_jec20_MAT_anone
MFalphacore MATgene modelexonerate100.0cov 100.0%2.3e-2080 bits232,996–233,109 -140410_jec21_MAT_alphanone
RPL39core MAThit onlyDIAMOND, proteome100.0cov 98.0%3.4e-34100 bits245,597–245,876 -–40410_jec20_MAT_aCNBD0680 RPL39alpha
PAN6conserved flankhit onlyDIAMOND, proteome100.0cov 100.0%5.7e-302806 bits266,145–267,812 +–40410_jec20_MAT_aCNBD0730 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
MATCM000041:394,220–395,678undeterminedSTE31too few of the family's genes found

Provenance

Genome file
CdeneoformansB-3501A.genome.fasta
Assembly
14 contigs · 19.7 Mb · N50 1.5 Mb
Genome SHA-256
a07f2fe85750548bc9b7e63fc3afce9bfe92b7d060dcb408209435bbbfa4d95b
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': ['high_N', 'identical_to_reference'], '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
2026-11-07T02:13:57Z
Run time
21 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