MATPredict · mating-type report

CneoformansVNII

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 CP091249alpha locus: genes from left to right on CP091249, 179,445 to 311,161: FAO1 (conserved flank, plus strand); SXI1 (core MAT gene, plus strand); STE3 (core MAT gene, plus strand); MFa (core MAT gene, minus strand); MFalpha (core MAT gene, minus strand); RPL39 (core MAT gene, plus strand); PAN6 (conserved flank, plus strand).200 kb250 kb300 kb← 172.9 kb more to contig endcalled locusFAO1: conserved flank, 179,445–180,804 (+), identity 90.2%, search hit onlyFAO1SXI1: core MAT gene, 181,584–182,945 (+), identity 81.2%, search hit onlySXI1STE3: core MAT gene, 196,706–198,026 (+), identity 75.0%, search hit onlySTE3MFa: core MAT gene, 224,052–224,165 (-), identity 52.381%, search hit onlyMFa (lost to MFalpha)MFalpha: core MAT gene, 224,052–224,165 (-), identity 86.84%, gene modelMFalphaRPL39: core MAT gene, 295,120–295,375 (+), identity 92.16%, gene modelRPL39PAN6: conserved flank, 309,266–311,161 (+), identity 84.3%, search hit onlyPAN6
Gene order on CP091249. Scroll sideways to see the whole figure.
FungiDB release 71 gene models on CP091249, 172,869 to 317,740LQV05_003234 170,940-173,894 (+): Fungal specific transcription factor domain | domain-containing proteinLQV05_003234LQV05_003235 174,577-176,762 (-): Permease family | domain-containing proteinLQV05_003235LQV05_003236 177,794-178,873 (-): Cytidine and deoxycytidylate deaminase zinc-binding region | domain-containing proteinLQV05_003236LQV05_003237 179,445-180,804 (+): 2OG-Fe(II) oxygenase superfamily | non-haem dioxygenase in morphine synthesis N-terminal | domain-containing proteinLQV05_003237LQV05_003238 181,584-182,945 (+): Homeobox KN domain | domain-containing proteinLQV05_003238LQV05_003239 184,100-186,352 (-): Glycosyl transferase family 90 | domain-containing proteinLQV05_003239LQV05_003240 186,887-190,563 (+): Kyakuja-Dileera-Zisupton transposase | CxC1 like cysteine cluster associated with KDZ transposases | domain-containing proteinLQV05_003240LQV05_003241 192,687-194,113 (-): Electron transfer flavoprotein FAD-binding domain | Electron transfer flavoprotein domain | domain-containing proteinLQV05_003241LQV05_003242 194,720-195,850 (+): unspecified productLQV05_003242LQV05_003243 196,706-198,026 (+): Pheromone A receptor | domain-containing proteinLQV05_003243LQV05_003244 199,172-201,818 (+): Protein kinase domain | domain-containing proteinLQV05_003244LQV05_003245 202,461-203,049 (-): unspecified productLQV05_003245LQV05_003246 204,640-205,254 (-): Ribosomal L22e protein family | domain-containing proteinLQV05_003246LQV05_003247 205,758-211,952 (+): Phospholipase D Active site motif | domain-containing proteinLQV05_003247LQV05_003248 213,794-215,388 (+): unspecified productLQV05_003248LQV05_003249 219,001-221,592 (-): BTB/POZ domain | domain-containing proteinLQV05_003249LQV05_003250 226,321-230,002 (+): BAH domain | domain-containing proteinLQV05_003250LQV05_003251 230,130-230,821 (-): eukaryotic translation initiation factor 3 subunit BLQV05_003251LQV05_003252 231,017-232,785 (-): eukaryotic translation initiation factor 3 subunit BLQV05_003252LQV05_003253 236,127-241,961 (+): DIL domain | Myosin head (motor domain) | domain-containing proteinLQV05_003253LQV05_003254 242,591-244,813 (-): non-specific serine/threonine protein kinaseLQV05_003254LQV05_003255 245,658-249,645 (+): Protein kinase domain | SAM domain (Sterile alpha motif) | Ras-binding domain of Byr2 | domain-containing proteinLQV05_003255LQV05_003256 250,088-254,462 (-): DNA-directed RNA polymeraseLQV05_003256LQV05_003257 254,709-257,429 (+): unspecified productLQV05_003257LQV05_003258 257,559-259,632 (-): dihydrolipoyl dehydrogenaseLQV05_003258LQV05_003259 259,936-262,882 (-): Poly(A) RNA polymerase, mitochondrial-like, central palm domain | Cid1 family poly A polymerase | domain-containing proteinLQV05_003259LQV05_003260 263,883-267,052 (-): RhoGEF domain | domain-containing proteinLQV05_003260LQV05_003261 268,421-272,118 (-): Kyakuja-Dileera-Zisupton transposase | CxC1 like cysteine cluster associated with KDZ transposases | domain-containing proteinLQV05_003261LQV05_003262 274,856-276,457 (+): unspecified productLQV05_003262LQV05_003263 276,700-277,561 (-): unspecified productLQV05_003263LQV05_003264 279,190-285,180 (+): [histone H3]-trimethyl-L-lysine4 demethylaseLQV05_003264LQV05_003265 285,776-288,502 (+): Slx4 endonuclease | domain-containing proteinLQV05_003265LQV05_003266 289,081-290,142 (-): DDE superfamily endonuclease | domain-containing proteinLQV05_003266LQV05_003267 296,853-301,263 (-): Zinc finger, C2H2 type | STE like transcription factor | domain-containing proteinLQV05_003267LQV05_003268 302,735-303,257 (-): unspecified productLQV05_003268LQV05_003269 304,232-305,333 (+): unspecified productLQV05_003269LQV05_003270 306,058-309,048 (+): nucleolar GTP-binding protein 2LQV05_003270LQV05_003271 309,266-311,161 (+): pantoate-beta-alanine ligaseLQV05_003271LQV05_003272 311,364-314,012 (-): unspecified productLQV05_003272LQV05_003273 316,369-319,916 (-): Autophagy protein ATG9 | domain-containing proteinLQV05_003273
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
CP091249:179,445–311,161 · 131.7 kb
Own genes
CP091249:179,445–311,161 · 131.7 kb
Locus
Complete locus: MAT gene(s) with their flanking genes.
Genes modelled
6 of 7 gene hits
Nearest contig end
179.4 kb
Region (samtools)
CP091249:179445-311161
Idiomorph scores
  • alpha 617.0

Margin over the set-aside MFa hit: 34.5 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
MFalpha86.8MFa52.4100.0higher identity
MFalpha86.8MFa52.4100.0higher identity
MFalpha86.8MFa52.4100.0higher identity
MFalpha86.8MFa52.4100.0higher identity

Gene evidence

GeneRoleModel Identity %E-value Position (strand)Exons Reference recordFungiDB gene
FAO1conserved flankhit onlyDIAMOND, proteome90.2cov 100.0%2.4e-232624 bits179,445–180,804 +–40410_jec20_MAT_aLQV05_003237
SXI1core MAThit onlyDIAMOND, proteome81.2cov 100.0%4.5e-227617 bits181,584–182,945 +–40410_jec21_MAT_alphaLQV05_003238
STE3core MAThit onlyDIAMOND, proteome75.0cov 100.0%4.8e-198538 bits196,706–198,026 +–40410_jec21_MAT_alphaLQV05_003243
MFacore MATlost to MFalpha, not countedhit onlytblastn52.4cov 100.0%1.1e-0127 bits224,052–224,165 -–40410_jec20_MAT_anone
MFalphacore MATgene modelexonerate86.8cov 100.0%1.9e-1257 bits224,052–224,165 -140410_jec21_MAT_alphanone
RPL39core MATgene modelexonerate92.2cov 100.0%1.2e-1667 bits295,120–295,375 +240410_jec20_MAT_anone
PAN6conserved flankhit onlyDIAMOND, proteome84.3cov 100.0%3.1e-243658 bits309,266–311,161 +–40410_jec20_MAT_aLQV05_003271
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
MATCP091250:404,548–406,005undeterminedSTE31too few of the family's genes found

Provenance

Genome file
CneoformansVNII.genome.fasta
Assembly
14 contigs · 19.0 Mb · N50 1.4 Mb
Genome SHA-256
5fcd966a044edf9814a0886f59c64f85681add2eb914be29057418f2be6c93e7
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
2026-11-07T02:20:23Z
Run time
19 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