MATPredict · mating-type report

CneoformansKN99

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 02:20 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 CP022325.1alpha locus: genes from left to right on CP022325.1, 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 CP022325.1. Scroll sideways to see the whole figure.
FungiDB release 71 gene models on CP022325.1, 178,711 to 291,866CKF44_06818 175,237-178,834 (+): Fungal specific transcription factor domain | domain-containing proteinCKF44_06818CKF44_06817 178,722-181,616 (-): NCS2 family nucleobase:cation symporter-2CKF44_06817CKF44_06816 182,119-185,466 (-): Cytidine and deoxycytidylate deaminase zinc-binding region | domain-containing proteinCKF44_06816CKF44_06815 183,564-185,652 (+): 2OG-Fe(II) oxygenase superfamily | non-haem dioxygenase in morphine synthesis N-terminal | domain-containing proteinCKF44_06815CKF44_06814 185,700-188,859 (+): Homeobox KN domain | domain-containing proteinCKF44_06814CKF44_06813 189,560-192,241 (-): Glycosyl transferase family 90 | domain-containing proteinCKF44_06813CKF44_06812 193,324-200,779 (-): phospholipase DCKF44_06812CKF44_06811 200,909-202,001 (+): large subunit ribosomal protein L22eCKF44_06811CKF44_06810 202,602-204,039 (+): hypothetical proteinCKF44_06810CKF44_06809 204,044-207,447 (-): IKS protein kinaseCKF44_06809CKF44_06808 208,236-209,840 (-): pheromone a factor receptorCKF44_06808CKF44_06807 210,557-211,580 (-): hypothetical proteinCKF44_06807CKF44_06806 212,068-213,909 (+): electron transfer flavoprotein alpha subunitCKF44_06806CKF44_06805 214,530-215,070 (+): hypothetical proteinCKF44_06805CKF44_06804 215,850-219,594 (-): BTB/POZ domain | domain-containing proteinCKF44_06804CKF44_07406 222,288-222,701 (-): pheromone alphaCKF44_07406CKF44_07407 222,704-223,314 (+): fungal mating-type pheromoneCKF44_07407CKF44_06971 223,846-230,310 (+): IQ calmodulin-binding motif | DIL domain | Myosin head (motor domain) | domain-containing proteinCKF44_06971CKF44_07408 230,211-233,167 (-): STE/STE20/PAKA protein kinaseCKF44_07408CKF44_06980 233,496-238,299 (+): STE/STE11 protein kinaseCKF44_06980CKF44_07409 238,263-242,729 (-): DNA-directed RNA polymerase, mitochondrialCKF44_07409CKF44_07005 242,901-246,213 (+): hypothetical proteinCKF44_07005CKF44_07004 244,073-247,927 (-): dihydrolipoyl dehydrogenaseCKF44_07004CKF44_07410 248,015-251,440 (-): Cid1 family poly A polymerase | Poly(A) RNA polymerase, mitochondrial-like, central palm domain | domain-containing proteinCKF44_07410CKF44_07015 251,935-255,597 (-): RhoGEF domain | domain-containing proteinCKF44_07015CKF44_07411 256,515-263,236 (+): histone demethylase JARID1CKF44_07411CKF44_01457 263,567-266,561 (+): Slx4 endonuclease | domain-containing proteinCKF44_01457CKF44_01456 267,859-269,211 (+): hypothetical proteinCKF44_01456CKF44_01455 270,518-271,941 (+): large subunit ribosomal protein L39CKF44_01455CKF44_01454 271,944-275,730 (-): transcription factor STE12CKF44_01454CKF44_07412 277,218-277,511 (-): hypothetical proteinCKF44_07412CKF44_01452 280,007-281,233 (+): hypothetical proteinCKF44_01452CKF44_01451 280,948-281,513 (-): hypothetical proteinCKF44_01451CKF44_07413 281,653-284,758 (+): nucleolar GTP-binding protein 2CKF44_07413CKF44_07414 284,872-286,790 (+): pantoate-beta-alanine ligaseCKF44_07414CKF44_01448 286,747-290,119 (-): hypothetical proteinCKF44_01448CKF44_01446 290,468-291,329 (-): Heat shock protein 9/12 | domain-containing proteinCKF44_01446CKF44_01445 291,364-295,513 (-): autophagy-like protein 9CKF44_01445
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
CP022325.1:183,859–286,720 · 102.9 kb
Own genes
CP022325.1:183,859–286,720 · 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)
CP022325.1:183859-286720
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_aCKF44_06816 (opposite strand)
CKF44_06815
SXI1core MAThit onlyDIAMOND, proteome80.7cov 100.0%7.8e-228619 bits185,988–187,349 +–40410_jec21_MAT_alphaCKF44_06814
STE3core MAThit onlyDIAMOND, proteome94.5cov 100.0%9.1e-265710 bits208,374–209,695 -–40410_jec21_MAT_alphaCKF44_06808
MFacore MATlost to MFalpha, not countedhit onlytblastn52.4cov 100.0%1.1e-0127 bits222,503–222,616 -–40410_jec20_MAT_aCKF44_07406
MFalphacore MAThit onlyDIAMOND, proteome86.8cov 100.0%4.2e-2167 bits222,931–223,047 +–40410_jec21_MAT_alphaCKF44_07407
RPL39core MAThit onlyDIAMOND, proteome100.0cov 100.0%2.1e-35103 bits270,550–271,048 +–40410_jec20_MAT_aCKF44_01455
PAN6conserved flankhit onlyDIAMOND, proteome92.0cov 100.0%2.4e-274737 bits284,943–286,720 +–40410_jec20_MAT_aCKF44_07414
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
MATCP022322.1:1,226,371–1,227,827undeterminedSTE31too few of the family's genes found

Provenance

Genome file
CneoformansKN99.genome.fasta
Assembly
15 contigs · 18.9 Mb · N50 1.4 Mb
Genome SHA-256
4268fe85d5d5ee6e8f1f0a195f38d6010789fc0a796ee1ab3be029603efd025a
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
2026-11-07T02:20:00Z
Run time
22 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