MATPredict · mating-type report

Ccf.gattiiMF34

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 02:12 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 CM018868alpha locus: genes from left to right on CM018868, 59,680 to 262,446: FAO1 (conserved flank, plus strand); SXI2 (core MAT gene, minus 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, minus strand); PAN6 (conserved flank, plus strand).50 kb100 kb150 kb200 kb250 kb← 49.5 kb more to contig endcalled locusFAO1: conserved flank, 146,033–147,380 (+), identity 85.2%, search hit onlyFAO1SXI2: core MAT gene, 147,892–148,082 (-), identity 70.97%, gene modelSXI2SXI1: core MAT gene, 148,521–151,835 (+), identity 71.7%, search hit onlySXI1STE3: core MAT gene, 224,262–228,685 (+), identity 92.6%, search hit onlySTE3MFa: core MAT gene, 229,842–229,955 (-), identity 54.762%, search hit onlyMFa (lost to MFalpha)MFalpha: core MAT gene, 229,842–229,955 (-), identity 94.74%, gene modelMFalphaRPL39: core MAT gene, 248,437–254,192 (-), identity 98.0%, search hit onlyRPL39PAN6: conserved flank, 260,700–262,446 (+), identity 91.5%, search hit onlyPAN6
Gene order on CM018868. Scroll sideways to see the whole figure.
FungiDB release 71 gene models on CM018868, 49,531 to 272,576D1P53_003234 48,889-49,845 (-): DDE superfamily endonuclease | domain-containing proteinD1P53_003234D1P53_003235 50,934-51,705 (-): unspecified productD1P53_003235D1P53_003236 52,210-57,774 (+): Protein kinase domain | domain-containing proteinD1P53_003236D1P53_003237 59,558-63,409 (+): Peroxisomal ATPase PEX1D1P53_003237D1P53_003238 64,020-66,912 (-): elongation factor 2D1P53_003238D1P53_003239 69,433-69,515 (-): tRNA-TrpD1P53_003239D1P53_003240 69,998-71,181 (-): Phospholipid methyltransferase | domain-containing proteinD1P53_003240D1P53_003241 71,763-74,000 (+): RNA helicaseD1P53_003241D1P53_003242 74,813-77,142 (+): PH domain | domain-containing proteinD1P53_003242D1P53_003243 77,486-79,239 (-): Oxidoreductase family, C-terminal alpha/beta domain | Oxidoreductase family, NAD-binding Rossmann fold | domain-containing proteinD1P53_003243D1P53_003244 81,632-83,976 (+): Beta-glucan synthesis-associated protein SKN1/KRE6/Sbg1 | domain-containing proteinD1P53_003244D1P53_003245 84,252-87,437 (-): dolichyl-phosphate-mannose-protein mannosyltransferaseD1P53_003245D1P53_003246 92,103-94,269 (+): Beta-glucan synthesis-associated protein SKN1/KRE6/Sbg1 | domain-containing proteinD1P53_003246D1P53_003247 95,092-97,836 (-): histidinol dehydrogenaseD1P53_003247D1P53_003248 98,192-100,000 (-): squalene monooxygenaseD1P53_003248D1P53_003249 101,567-104,432 (+): Transmembrane amino acid transporter protein | domain-containing proteinD1P53_003249D1P53_003250 105,675-106,865 (+): Protein of unknown function (DUF3760) | domain-containing proteinD1P53_003250D1P53_003251 108,434-110,454 (+): YL1 nuclear protein | YL1 nuclear protein C-terminal domain | domain-containing proteinD1P53_003251D1P53_003252 111,006-112,777 (-): Eukaryotic integral membrane protein (DUF1751) | domain-containing proteinD1P53_003252D1P53_003253 112,956-115,709 (+): LisH | WD domain, G-beta repeat | domain-containing proteinD1P53_003253D1P53_003254 116,571-117,308 (+): unspecified productD1P53_003254D1P53_003255 117,547-120,248 (-): unspecified productD1P53_003255D1P53_003256 121,094-123,438 (-): ferric-chelate reductase (NADPH)D1P53_003256D1P53_003257 124,785-125,639 (+): unspecified productD1P53_003257D1P53_003258 125,889-132,158 (-): Chromatin-remodeling ATPase INO80D1P53_003258D1P53_003259 134,523-137,294 (-): unspecified productD1P53_003259D1P53_003260 137,675-140,569 (+): Fungal specific transcription factor domain | domain-containing proteinD1P53_003260D1P53_003261 141,300-143,467 (-): Permease family | domain-containing proteinD1P53_003261D1P53_003262 144,379-145,456 (-): Cytidine and deoxycytidylate deaminase zinc-binding region | domain-containing proteinD1P53_003262D1P53_003263 146,033-147,380 (+): non-haem dioxygenase in morphine synthesis N-terminal | 2OG-Fe(II) oxygenase superfamily | domain-containing proteinD1P53_003263D1P53_003264 148,521-151,835 (+): Homeobox KN domain | Ribosomal L22e protein family | domain-containing proteinD1P53_003264D1P53_003265 153,263-159,236 (+): [histone H3]-trimethyl-L-lysine4 demethylaseD1P53_003265D1P53_003266 160,130-162,515 (+): unspecified productD1P53_003266D1P53_003267 163,772-166,944 (+): RhoGEF domain | domain-containing proteinD1P53_003267D1P53_003268 167,440-174,038 (-): Phospholipase D Active site motif | domain-containing proteinD1P53_003268D1P53_003269 175,600-177,843 (-): Glycosyl transferase family 90 | domain-containing proteinD1P53_003269D1P53_003270 179,664-182,614 (+): Cid1 family poly A polymerase | Poly(A) RNA polymerase, mitochondrial-like, central palm domain | domain-containing proteinD1P53_003270D1P53_003271 183,075-185,142 (+): dihydrolipoyl dehydrogenaseD1P53_003271D1P53_003272 185,271-187,968 (-): unspecified productD1P53_003272D1P53_003273 188,224-192,597 (+): DNA-directed RNA polymeraseD1P53_003273D1P53_003274 192,993-196,954 (-): Protein kinase domain | SAM domain (Sterile alpha motif) | Ras-binding domain of Byr2 | domain-containing proteinD1P53_003274D1P53_003275 197,951-203,782 (+): DIL domain | Myosin head (motor domain) | domain-containing proteinD1P53_003275D1P53_003276 204,336-206,743 (-): non-specific serine/threonine protein kinaseD1P53_003276D1P53_003277 207,601-212,846 (-): Glycosyl transferase family group 2 | domain-containing proteinD1P53_003277D1P53_003278 213,128-216,310 (+): Glycosyl transferase family group 2 | domain-containing proteinD1P53_003278D1P53_003279 221,132-222,557 (-): Electron transfer flavoprotein domain | Electron transfer flavoprotein FAD-binding domain | domain-containing proteinD1P53_003279D1P53_003280 224,262-228,685 (+): Protein kinase domain | Pheromone A receptor | domain-containing proteinD1P53_003280D1P53_003281 234,020-236,777 (+): unspecified productD1P53_003281D1P53_003282 236,918-239,577 (-): eukaryotic translation initiation factor 3 subunit BD1P53_003282D1P53_003283 244,581-246,711 (+): BTB/POZ domain | domain-containing proteinD1P53_003283D1P53_003284 248,437-254,192 (-): 60S ribosomal protein L39D1P53_003284D1P53_003285 255,865-256,944 (+): unspecified productD1P53_003285D1P53_003286 257,596-260,423 (+): nucleolar GTP-binding protein 2D1P53_003286D1P53_003287 260,700-262,446 (+): pantoate-beta-alanine ligaseD1P53_003287D1P53_003288 262,650-265,275 (-): unspecified productD1P53_003288D1P53_003289 267,679-271,208 (-): Autophagy protein ATG9 | domain-containing proteinD1P53_003289D1P53_003290 271,445-272,184 (+): RNA polymerase Rpb4 | domain-containing proteinD1P53_003290D1P53_003291 272,346-275,849 (-): cysteine desulfurase IscSD1P53_003291
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
  • The locus is longer than this family's usual span. Large loci are real; check the figure.
Location
CM018868:59,680–262,446 · 202.8 kb
Own genes
CM018868:146,033–262,446 · 116.4 kb · the span runs 86.4 kb beyond these genes
Supported span
CM018868:146,033–262,446 · 116.4 kb · 86.4 kb of the reported span rests only on hits below 33 bits
Locus
Complete locus: MAT gene(s) with their flanking genes.
Genes modelled
7 of 8 gene hits
Nearest contig end
59.7 kb
Region (samtools)
CM018868:59680-262446
Idiomorph scores
  • alpha 553.0
  • a 48.5

Margin over the next idiomorph: 504.5

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
MFalpha94.7MFa54.8100.0higher identity
MFalpha94.7MFa54.8100.0higher identity
MFalpha94.7MFa54.8100.0higher identity
MFalpha94.7MFa54.8100.0higher identity

Gene evidence

GeneRoleModel Identity %E-value Position (strand)Exons Reference recordFungiDB gene
FAO1conserved flankhit onlyDIAMOND, proteome85.2cov 100.0%8.8e-219589 bits146,033–147,380 +–40410_jec20_MAT_aD1P53_003263
SXI2core MATgene modelexonerate2 frameshiftsdefective gene model71.0cov 9.0%9.6e-0648 bits147,892–148,082 -140410_jec20_MAT_anone
SXI1core MAThit onlyDIAMOND, proteome71.7cov 99.3%4.2e-200553 bits148,521–151,835 +–40410_jec21_MAT_alphaD1P53_003264
STE3core MAThit onlyDIAMOND, proteome92.6cov 14.2%6.9e-31114 bits224,262–228,685 +–40410_jec21_MAT_alphaD1P53_003280
MFacore MATlost to MFalpha, not countedhit onlytblastn54.8cov 100.0%2.2e-0640 bits229,842–229,955 -–40410_jec20_MAT_anone
MFalphacore MATgene modelexonerate94.7cov 100.0%9.8e-1975 bits229,842–229,955 -140410_jec21_MAT_alphanone
RPL39core MAThit onlyDIAMOND, proteome98.0cov 100.0%3.9e-30102 bits248,437–254,192 -–40410_jec20_MAT_aD1P53_003284
PAN6conserved flankhit onlyDIAMOND, proteome91.5cov 100.0%1.2e-268723 bits260,700–262,446 +–40410_jec20_MAT_aD1P53_003287
MFanot searchable: no reference protein in the database–
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
MATCM018866:411,360–412,802undeterminedSTE31too few of the family's genes found

Provenance

Genome file
Ccf.gattiiMF34.genome.fasta
Assembly
15 contigs · 17.9 Mb · N50 1.3 Mb
Genome SHA-256
9593d027aef3bd04e05ab844ab908f85948dbde6abde658fca95339b5b9e52ab
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': ['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
2026-11-07T02:12:11Z
Run time
20 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