MATPredict · mating-type report

CgattiiWM276

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 CP000294alpha locus: genes from left to right on CP000294, 153,061 to 274,435: FAO1 (conserved flank, plus strand); SXI2 (core MAT gene, minus strand); SXI1 (core MAT gene, plus strand); STE3 (core MAT gene, plus strand); MFalpha (core MAT gene, minus strand); MFa (core MAT gene, minus strand); RPL39 (core MAT gene, minus strand); PAN6 (conserved flank, plus strand).160 kb180 kb200 kb220 kb240 kb260 kb280 kb← 147.0 kb more to contig endcalled locusFAO1: conserved flank, 153,061–154,411 (+), identity 90.2%, search hit onlyFAO1SXI2: core MAT gene, 154,925–155,112 (-), identity 59.68%, gene modelSXI2SXI1: core MAT gene, 155,558–156,917 (+), identity 71.2%, search hit onlySXI1STE3: core MAT gene, 234,136–235,454 (+), identity 90.8%, search hit onlySTE3MFalpha: core MAT gene, 240,435–240,551 (-), identity 94.7%, search hit onlyMFalphaMFa: core MAT gene, 240,438–240,551 (-), identity 54.762%, search hit onlyMFa (lost to MFalpha)RPL39: core MAT gene, 260,428–260,927 (-), identity 100.0%, search hit onlyRPL39PAN6: conserved flank, 272,753–274,435 (+), identity 90.5%, search hit onlyPAN6
Gene order on CP000294. Scroll sideways to see the whole figure.
FungiDB release 71 gene models on CP000294, 146,988 to 280,502CGB_I0470W 144,706-147,597 (+): Zn2-Cys6 transcription factorCGB_I0470W HAP1CGB_I0480C 148,352-150,520 (-): uric acid xanthine permeaseCGB_I0480C UAP1CGB_I0490C 151,411-152,490 (-): cytosine deaminaseCGB_I0490CCGB_I0500W 153,061-154,411 (+): putative fatty alcohol oxidase in the mating-type locusCGB_I0500W FAO1CGB_I0510W 155,558-156,917 (+): alpha cell-type homeodomain transcription factorCGB_I0510W SXI1alphaCGB_I0520W 158,301-158,984 (+): SWIM zinc finger | domain-containing proteinCGB_I0520WCGB_I0530C 160,075-161,192 (-): hypothetical ProteinCGB_I0530CCGB_I0540W 162,558-164,049 (+): hypothetical ProteinCGB_I0540WCGB_I0550W 164,129-165,742 (+): hypothetical proteinCGB_I0550WCGB_I0560W 166,088-166,336 (+): hypothetical ProteinCGB_I0560WCGB_I0570W 166,832-167,433 (+): large subunit ribosomal protein L22eCGB_I0570W RPL22alphaCGB_I0580C 167,472-168,136 (-): protein-Golgi retention-related proteinCGB_I0580CCGB_I0590W 168,889-174,864 (+): phd transcription factorCGB_I0590W RUM1alphaCGB_I0600W 175,768-178,510 (+): Structure-specific endonuclease subunit SLX4CGB_I0600W BSP1CGB_I0610W 179,390-182,561 (+): RhoGEF domain | domain-containing proteinCGB_I0610WCGB_I0620C 183,788-189,361 (-): phospholipase D1CGB_I0620C SPO14alphaCGB_I0630C 191,191-193,434 (-): O-glucosyltransferaseCGB_I0630C CAP1alphaCGB_I0640W 195,065-198,017 (+): cid1-family polyA polymeraseCGB_I0640W CID1alphaCGB_I0650W 198,514-200,531 (+): putative dihydrolipoyl dehydrogenaseCGB_I0650W LPD1alphaCGB_I1005C 201,278-205,133 (-): hypothetical ProteinCGB_I1005CCGB_I1010W 206,688-206,903 (+): unspecified productCGB_I1010WCGB_I1020C 207,015-209,733 (-): armadillo/beta-catenin repeat protein, encoded on mat locusCGB_I1020C BSP2CGB_I1030W 210,345-214,352 (+): DNA-directed mRNA polymerase, mitochondrialCGB_I1030W RPO41alphaCGB_I1040C 215,078-219,044 (-): mapkk kinase, ste/ste11 protein kinaseCGB_I1040C STE11alphaCGB_I1050W 220,067-225,897 (+): myosin class v heavy chainCGB_I1050W MYO2alphaCGB_I1060C 226,496-228,860 (-): ste/ste20/paka protein kinaseCGB_I1060C STE20alphaCGB_I1070C 229,604-229,901 (-): hypothetical ProteinCGB_I1070CCGB_I1080C 231,542-232,971 (-): electron transfer flavoprotein alpha subunitCGB_I1080C ETF1alphaCGB_I1090W 234,136-235,454 (+): a-factor pheromone receptorCGB_I1090W STE3alphaCGB_I1100W 236,640-239,303 (+): serine/threonine-protein kinaseCGB_I1100W IKS1CGB_I1110C 240,435-240,551 (-): MFalpha1 proteinCGB_I1110CCGB_I1120W 241,313-241,429 (+): MFalpha2 proteinCGB_I1120WCGB_I1130W 242,485-245,147 (+): eukaryotic translation initiation factor PRT1pCGB_I1130WCGB_I1140C 245,289-248,804 (-): ZNF1pCGB_I1140CCGB_I1150C 251,792-251,908 (-): mating-type pheromone alphaCGB_I1150C MFalpha3CGB_I1160W 252,670-252,786 (+): MFalpha4pCGB_I1160WCGB_I1180W 257,940-259,301 (+): btp/pz domain proteinCGB_I1180W BSP3CGB_I1190C 260,428-260,927 (-): large subunit ribosomal protein L39CGB_I1190C RPL39alphaCGB_I1200C 263,025-266,130 (-): ste-like transcription factorCGB_I1200C STE12alphaCGB_I1210W 267,832-268,910 (+): mat3 pheromone repeat proteinCGB_I1210W MAT3CGB_I1220W 269,539-272,403 (+): putative nucleolar gtp-binding proteinCGB_I1220W NOG2CGB_I1230W 272,753-274,435 (+): pantoate-beta-alanine ligaseCGB_I1230W PAN6CGB_I1240C 274,637-277,262 (-): hypothetical proteinCGB_I1240CCGB_I1250C 278,197-278,618 (-): heat shock protein, 12KdaCGB_I1250C HSP12CGB_I1260W 278,700-279,158 (+): hypothetical ProteinCGB_I1260WCGB_I1270C 279,606-282,673 (-): autophagy-related proteinCGB_I1270C 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
CP000294:153,061–274,435 · 121.4 kb
Own genes
CP000294:153,061–274,435 · 121.4 kb
Locus
Complete locus: MAT gene(s) with their flanking genes.
Genes modelled
7 of 8 gene hits
Nearest contig end
153.1 kb
Region (samtools)
CP000294:153061-274435
Idiomorph scores
  • alpha 541.0
  • a 40.8

Margin over the next idiomorph: 500.2

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, proteome90.2cov 100.0%2.8e-238639 bits153,061–154,411 +–40410_jec20_MAT_aCGB_I0500W FAO1
SXI2core MATgene modelexonerate2 frameshiftsdefective gene model59.7cov 8.9%9.9e-0941 bits154,925–155,112 -140410_jec20_MAT_anone
SXI1core MAThit onlyDIAMOND, proteome71.2cov 100.0%3.1e-197541 bits155,558–156,917 +–40410_jec21_MAT_alphaCGB_I0510W SXI1alpha
STE3core MAThit onlyDIAMOND, proteome90.8cov 100.0%1.2e-262704 bits234,136–235,454 +–40410_jec21_MAT_alphaCGB_I1090W STE3alpha
MFalphacore MAThit onlyDIAMOND, proteome94.7cov 100.0%3.1e-2372 bits240,435–240,551 -–40410_jec21_MAT_alphaCGB_I1110C
MFacore MATlost to MFalpha, not countedhit onlytblastn54.8cov 100.0%2.2e-0640 bits240,438–240,551 -–40410_jec20_MAT_aCGB_I1110C
RPL39core MAThit onlyDIAMOND, proteome100.0cov 100.0%2.1e-35103 bits260,428–260,927 -–40410_jec20_MAT_aCGB_I1190C RPL39alpha
PAN6conserved flankhit onlyDIAMOND, proteome90.5cov 100.0%7.4e-267717 bits272,753–274,435 +–40410_jec20_MAT_aCGB_I1230W PAN6
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
MATCP000286:368,005–369,433undeterminedSTE31too few of the family's genes found

Provenance

Genome file
CgattiiWM276.genome.fasta
Assembly
14 contigs · 18.4 Mb · N50 1.3 Mb
Genome SHA-256
9e1bab3e2b2afa498cba712a7cc48841e61a38f03a3df631f39846dcd14e5e1b
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
2026-11-07T02:19:41Z
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