MATPredict · mating-type report

ScerevisiaeS288C

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 01:58 UTC by MATPredict 0.8.1

Result

Mating-type loci

MATahigh confidenceMATalphamedium confidenceMATalphamedium confidence

Called loci 3

MATa MATsc family · Ascomycota

high confidence
Gene order of the MATa locus on BK006937MATa locus: genes from left to right on BK006937, 293,179 to 294,494: MATA2 (core MAT gene, minus strand); MATALPHA2 (core MAT gene, minus strand); MATA1 (core MAT gene, plus strand); MATALPHA1 (core MAT gene, plus strand).293.0 kb293.5 kb294.0 kb294.5 kb21.8 kb more to contig end →called locusMATA2: core MAT gene, 293,179–293,538 (-), identity 100.0%, search hit onlyMATA2MATALPHA2: core MAT gene, 293,179–293,538 (-), identity 100.0%, search hit onlyMATALPHA2MATA1: core MAT gene, 293,835–294,321 (+), identity 100.0%, search hit onlyMATA1MATALPHA1: core MAT gene, 294,375–294,494 (+), identity 95.0%, the two modelling tools disagreeMATALPHA1
Gene order on BK006937. Scroll sideways to see the whole figure.
FungiDB release 68 gene models on BK006937, 292,879 to 294,794YCR096C 293,179-293,538 (-): homeodomain mating type protein a2YCR096C HMRA2YCR097W 293,835-294,321 (+): Hmra1pYCR097W HMRA1
FungiDB release 68 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
  • tools disagree
  • alternate model
  • search hit only
Location
BK006937:293,179–294,494 · 1.3 kb
Cross-lineage class
MAT1-2
Own genes
BK006937:293,179–294,494 · 1.3 kb
Locus
Genes of both idiomorphs at one locus.
Genes modelled
4 of 4 gene hits
Nearest contig end
22.1 kb
Region (samtools)
BK006937:293179-294494
Idiomorph scores
  • MATa 245.0
  • MATalpha 82.0

Margin over the next idiomorph: 163.0

Score: bitscore of the best core-gene hit for each idiomorph.

Gene evidence

GeneRoleModel Identity %E-value Position (strand)Exons Reference recordFungiDB gene
MATA2core MAThit onlyDIAMOND, proteome100.0cov 100.0%6.3e-85233 bits293,179–293,538 -–4932_s288c_MATsc_HMRaYCR096C HMRA2
MATALPHA2core MAThit onlyDIAMOND, proteome100.0cov 56.7%1.3e-83233 bits293,179–293,538 -–4932_s288c_MATsc_MATalphaYCR096C HMRA2
MATA1core MAThit onlyDIAMOND, proteome100.0cov 100.0%2.0e-89245 bits293,835–294,321 +–4932_s288c_MATsc_HMRaYCR097W HMRA1
MATALPHA1core MATmodels differexonerateminiprot: 294,390–294,497, 100.0%1 internal stopdefective gene model95.0cov 22.9%6.0e-1982 bits294,375–294,494 +14932_s288c_MATsc_MATalphanone
cha1not searchable: no reference protein in the database–

MATalpha MATsc family · Ascomycota

medium confidence
Gene order of the MATalpha locus on BK006937MATalpha locus: genes from left to right on BK006937, 12,386 to 13,809: MATA2 (core MAT gene, minus strand); MATALPHA2 (core MAT gene, minus strand); MATALPHA1 (core MAT gene, plus strand).12.5 kb13.0 kb13.5 kb14.0 kb← 12.1 kb more to contig endcalled locusMATA2: core MAT gene, 12,386–13,018 (-), identity 100.0%, search hit onlyMATA2MATALPHA2: core MAT gene, 12,386–13,018 (-), identity 100.0%, search hit onlyMATALPHA2MATALPHA1: core MAT gene, 13,282–13,809 (+), identity 100.0%, search hit onlyMATALPHA1
Gene order on BK006937. Scroll sideways to see the whole figure.
FungiDB release 68 gene models on BK006937, 12,086 to 14,109YCL068C 11,503-12,285 (-): hypothetical proteinYCL068CYCL067C 12,386-13,018 (-): homeodomain mating type protein alpha2YCL067C HMLALPHA2YCL066W 13,282-13,809 (+): transcriptional co-activator mating type protein alphaYCL066W HMLALPHA1
FungiDB release 68 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
  • search hit only
Location
BK006937:12,386–13,809 · 1.4 kb
Cross-lineage class
MAT1-1
Own genes
BK006937:12,386–13,809 · 1.4 kb
Locus
Genes of both idiomorphs at one locus.
Genes modelled
3 of 3 gene hits
Nearest contig end
12.4 kb
Region (samtools)
BK006937:12386-13809
Idiomorph scores
  • MATalpha 354.0

No other idiomorph scored.

Score: bitscore of the best core-gene hit for each idiomorph.

Gene evidence

GeneRoleModel Identity %E-value Position (strand)Exons Reference recordFungiDB gene
MATA2core MAThit onlyDIAMOND, proteome100.0cov 100.0%5.7e-84235 bits12,386–13,018 -–4932_s288c_MATsc_HMRaYCL067C HMLALPHA2
MATALPHA2core MAThit onlyDIAMOND, proteome100.0cov 100.0%1.2e-149404 bits12,386–13,018 -–4932_s288c_MATsc_MATalphaYCL067C HMLALPHA2
MATALPHA1core MAThit onlyDIAMOND, proteome100.0cov 100.0%7.8e-131354 bits13,282–13,809 +–4932_s288c_MATsc_MATalphaYCL066W HMLALPHA1
MATA1expected, not found–
cha1not searchable: no reference protein in the database–

MATalpha MATsc family · Ascomycota

medium confidence
Gene order of the MATalpha locus on BK006937MATalpha locus: genes from left to right on BK006937, 199,546 to 200,969: MATA2 (core MAT gene, minus strand); MATALPHA2 (core MAT gene, minus strand); MATALPHA1 (core MAT gene, plus strand).199.5 kb200.0 kb200.5 kb201.0 kb115.4 kb more to contig end →called locusMATA2: core MAT gene, 199,546–200,178 (-), identity 100.0%, search hit onlyMATA2MATALPHA2: core MAT gene, 199,546–200,178 (-), identity 100.0%, search hit onlyMATALPHA2MATALPHA1: core MAT gene, 200,442–200,969 (+), identity 100.0%, search hit onlyMATALPHA1
Gene order on BK006937. Scroll sideways to see the whole figure.
FungiDB release 68 gene models on BK006937, 199,246 to 201,269YCR038C 197,621-199,549 (-): Ras family guanine nucleotide exchange factor BUD5YCR038C BUD5YCR039C 199,546-200,178 (-): homeodomain mating type protein alpha2YCR039C MATALPHA2YCR040W 200,442-200,969 (+): transcriptional co-activator mating type protein alphaYCR040W MATALPHA1YCR041W 200,911-201,243 (+): hypothetical proteinYCR041WYCR042C 201,174-205,397 (-): Taf2pYCR042C TAF2
FungiDB release 68 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
  • search hit only
Location
BK006937:199,546–200,969 · 1.4 kb
Cross-lineage class
MAT1-1
Own genes
BK006937:199,546–200,969 · 1.4 kb
Locus
Genes of both idiomorphs at one locus.
Genes modelled
3 of 3 gene hits
Nearest contig end
115.7 kb
Region (samtools)
BK006937:199546-200969
Idiomorph scores
  • MATalpha 354.0

No other idiomorph scored.

Score: bitscore of the best core-gene hit for each idiomorph.

Gene evidence

GeneRoleModel Identity %E-value Position (strand)Exons Reference recordFungiDB gene
MATA2core MAThit onlyDIAMOND, proteome100.0cov 100.0%5.7e-84235 bits199,546–200,178 -–4932_s288c_MATsc_HMRaYCR038C BUD5
YCR039C MATALPHA2
MATALPHA2core MAThit onlyDIAMOND, proteome100.0cov 100.0%1.2e-149404 bits199,546–200,178 -–4932_s288c_MATsc_MATalphaYCR038C BUD5
YCR039C MATALPHA2
MATALPHA1core MAThit onlyDIAMOND, proteome100.0cov 100.0%7.8e-131354 bits200,442–200,969 +–4932_s288c_MATsc_MATalphaYCR040W MATALPHA1
YCR041W
MATA1expected, not found–
cha1not searchable: no reference protein in the database–

Withheld candidate loci 31

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: fewer than 2 genes could be modelled (31).

Show the 31 withheld loci

Withheld loci (31)

familylocationidiomorph genesmodelledreason
MATscBK006947:188,051–209,377undeterminedMATALPHA2, sla21fewer than 2 genes could be modelled
MATscBK006934:192,640–192,915MATalphaMATALPHA10fewer than 2 genes could be modelled
MATscBK006934:499,208–499,312undeterminedMATALPHA20fewer than 2 genes could be modelled
MATscBK006938:72,500–72,616MATalphaMATALPHA10fewer than 2 genes could be modelled
MATscBK006938:271,473–271,739MATaMATA10fewer than 2 genes could be modelled
MATscBK006938:480,906–481,169MATaMATA10fewer than 2 genes could be modelled
MATscBK006938:1,144,383–1,144,535MATaMATA10fewer than 2 genes could be modelled
MATscBK006938:1,273,025–1,273,126MATalphaMATALPHA10fewer than 2 genes could be modelled
MATscBK006938:1,299,866–1,300,120MATalphaMATALPHA10fewer than 2 genes could be modelled
MATscBK006938:1,361,471–1,361,626undeterminedMATALPHA20fewer than 2 genes could be modelled
MATscBK006946:221,940–222,131MATaMATA10fewer than 2 genes could be modelled
MATscBK006946:694,821–694,943undeterminedMATALPHA20fewer than 2 genes could be modelled
MATscBK006946:897,463–897,648MATalphaMATALPHA10fewer than 2 genes could be modelled
MATscBK006949:15,119–15,274MATalphaMATALPHA10fewer than 2 genes could be modelled
MATscBK006949:213,261–213,575undeterminedMATALPHA20fewer than 2 genes could be modelled
MATscBK006949:679,702–679,938undeterminedMATA20fewer than 2 genes could be modelled
MATscBK006948:942,522–942,716undeterminedMATA20fewer than 2 genes could be modelled
MATscBK006948:1,075,866–1,076,021MATalphaMATALPHA10fewer than 2 genes could be modelled
MATscBK006945:240,155–240,277MATalphaMATALPHA10fewer than 2 genes could be modelled
MATscBK006945:573,273–573,461MATalphaMATALPHA10fewer than 2 genes could be modelled
MATscBK006941:119,225–127,079undeterminedMATALPHA20fewer than 2 genes could be modelled
MATscBK006941:325,850–326,116undeterminedMATALPHA20fewer than 2 genes could be modelled
MATscBK006941:763,231–763,326MATaMATA10fewer than 2 genes could be modelled
MATscBK006941:907,908–908,015MATalphaMATALPHA10fewer than 2 genes could be modelled
MATscBK006936:406,755–406,928undeterminedMATALPHA20fewer than 2 genes could be modelled
MATscBK006936:432,021–434,201MATaMATA1, MATA20fewer than 2 genes could be modelled
MATscBK006936:566,017–566,154undeterminedMATA20fewer than 2 genes could be modelled
MATscBK006939:23,345–23,446MATaMATA10fewer than 2 genes could be modelled
MATscBK006939:296,155–296,310MATaMATA10fewer than 2 genes could be modelled
MATscBK006943:516,083–516,247MATaMATA10fewer than 2 genes could be modelled
MATscBK006944:49,069–49,266MATalphaMATALPHA10fewer than 2 genes could be modelled

Provenance

Genome file
ScerevisiaeS288C.genome.fasta
Assembly
17 contigs · 12.2 Mb · N50 924.4 kb
Genome SHA-256
514d409384fd10fc380903b37dd267b607cfb569f8ec7a8e56bee6d001e840ca
MATPredict
0.8.1 (v0.8.1, 3a62e6302b)
Database
86f18d232e4fe95d · 185 records
Taxonomy
local NCBI taxonomy snapshot 2026-10-01
Parameters
phylum=Ascomycota, phylum_guess={'requested': 'auto', 'status': 'ok', 'usable': True, 'reason': None, 'phylum': 'Ascomycota', 'phylum_taxid': 4890, 'deepest_rank': 'genus', 'routing_taxid': 4893, '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 Ascomycota', 'action': 'routed', 'weak_call_accepted': False, 'genetic_code': 1, 'genetic_code_from': 'family taxid 4893', 'routed_by': 'family taxid 4893 (direct)'}, 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
2026-11-07T01:58:27Z
Run time
17 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