MATPredict · mating-type report

PkudriavzeviiCBS573

MAT locus above the FungiDB annotation (gene by gene)

Ascomycota

Run by MATPredict 0.8.1 (v0.8.1, 3a62e6302b) · database 86f18d232e4f · local NCBI taxonomy snapshot 2026-10-01 · rendered 2026-11-07 02:49 UTC by MATPredict 0.8.1

Result

Mating type

MATamedium confidence

Called loci 1

MATa MATsc family · Ascomycota

medium confidence
Gene order of the MATa locus on CP028774MATa locus: genes from left to right on CP028774, 307,183 to 311,300: sla2 (conserved flank, plus strand); MATA1 (core MAT gene, minus strand); MATALPHA2 (core MAT gene, minus strand).307 kb308 kb309 kb310 kb311 kb← 306.9 kb more to contig endcalled locussla2: conserved flank, 307,183–310,401 (+), identity 35.1%, search hit onlysla2MATA1: core MAT gene, 310,491–311,300 (-), identity 57.5%, search hit onlyMATA1MATALPHA2: core MAT gene, 310,515–310,610 (-), identity 35.294%, search hit onlyMATALPHA2 (lost to MATA1)
Gene order on CP028774. Scroll sideways to see the whole figure.
FungiDB release 71 gene models on CP028774, 306,883 to 311,600C5L36_0B01560 306,404-306,947 (-): Translation initiation factor SUI1 | domain-containing proteinC5L36_0B01560C5L36_0B01570 307,183-310,401 (+): ANTH domain | I/LWEQ domain | domain-containing proteinC5L36_0B01570C5L36_0B01580 310,491-311,300 (-): Homeodomain | domain-containing proteinC5L36_0B01580C5L36_0B01585 311,575-312,245 (+): unspecified productC5L36_0B01585
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
  • The same genes also match: Ascomycota:MTL.
  • MATALPHA2 is a weak hit to the other idiomorph's gene and was not counted against the call.
Location
CP028774:307,183–311,300 · 4.1 kb
Cross-lineage class
MAT1-2
Own genes
CP028774:307,183–311,300 · 4.1 kb
Locus
Provisional: the call only tied the admission bar, or came from the relaxed pass.
Genes modelled
2 of 3 gene hits
Nearest contig end
307.2 kb
Region (samtools)
CP028774:307183-311300
Idiomorph scores
  • MATa 53.9

Margin over the set-aside MATALPHA2 hit: 22.2 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
MATA157.5MATALPHA235.3100.0higher identity

Gene evidence

GeneRoleModel Identity %E-value Position (strand)Exons Reference recordFungiDB gene
sla2conserved flankhit onlyDIAMOND, proteome35.1cov 79.1%1.5e-87288 bits307,183–310,401 +–28985_nrrl-y-1140_MATsc_MATaC5L36_0B01570
MATA1core MAThit onlyDIAMOND, proteome57.5cov 31.7%1.0e-1154 bits310,491–311,300 -–4932_s288c_MATsc_HMRaC5L36_0B01580
MATALPHA2core MATother idiomorph, not countedlost to MATA1, not countedhit onlytblastn35.3cov 15.0%1.1e+0027 bits310,515–310,610 -–28985_nrrl-y-1140_MATsc_HMLalphaC5L36_0B01580
MATA2expected, not found–
cha1not searchable: no reference protein in the database–

Withheld candidate loci 70

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 (65); too few of the family's genes found (5).

Show the 70 withheld loci

Withheld loci (70)

familylocationidiomorph genesmodelledreason
MATscCP028773:84,990–125,366MATalphaMATALPHA1, MATALPHA2, MATA20fewer than 2 genes could be modelled
MTLCP028773:84,990–125,366AMTLA10fewer than 2 genes could be modelled
MTLCP028773:203,106–206,261alphaMTLalpha10fewer than 2 genes could be modelled
MATscCP028773:203,106–206,261undeterminedMATALPHA20fewer than 2 genes could be modelled
MTLCP028773:279,901–280,029AMTLA20fewer than 2 genes could be modelled
MATscCP028773:420,752–420,844MATalphaMATALPHA10fewer than 2 genes could be modelled
MATscCP028773:953,661–967,928undeterminedMATALPHA2, MATA20fewer than 2 genes could be modelled
MATscCP028773:1,063,719–1,063,808undeterminedMATALPHA20fewer than 2 genes could be modelled
MTLCP028773:1,451,456–1,451,596alphaMTLalpha10fewer than 2 genes could be modelled
MATscCP028773:1,489,569–1,489,685MATalphaMATALPHA10fewer than 2 genes could be modelled
MTLCP028773:1,673,220–1,673,309alphaMTLalpha10fewer than 2 genes could be modelled
MATscCP028773:1,757,788–1,757,880MATalphaMATALPHA10fewer than 2 genes could be modelled
MATscCP028773:1,911,842–1,937,211MATalphaMATALPHA10fewer than 2 genes could be modelled
MTLCP028773:1,963,634–1,963,870AMTLA10fewer than 2 genes could be modelled
MTLCP028773:2,254,386–2,254,556AMTLA10fewer than 2 genes could be modelled
MATscCP028773:2,306,522–2,306,638MATalphaMATALPHA10fewer than 2 genes could be modelled
MATscCP028773:2,403,331–2,403,447undeterminedMATALPHA20fewer than 2 genes could be modelled
MATscCP028773:2,578,242–2,578,481MATalphaMATALPHA10fewer than 2 genes could be modelled
MTLCP028774:66,227–66,394alphaMTLalpha10fewer than 2 genes could be modelled
MTLCP028774:193,343–230,301AMTLA2, MTLalpha1, PIK11fewer than 2 genes could be modelled
MTLCP028774:307,183–311,300AMTLA11fewer than 2 genes could be modelled
MTLCP028774:440,500–453,604AMTLA2, MTLalpha10fewer than 2 genes could be modelled
MATscCP028774:756,579–756,914MATalphaMATALPHA10fewer than 2 genes could be modelled
MTLCP028774:964,500–964,613AMTLA10fewer than 2 genes could be modelled
MTLCP028774:1,021,467–1,021,592alphaMTLalpha10fewer than 2 genes could be modelled
MTLCP028774:1,432,113–1,432,244AMTLA20fewer than 2 genes could be modelled
MTLCP028774:1,766,173–1,766,292AMTLA20fewer than 2 genes could be modelled
MTLCP028774:1,899,269–1,899,430alphaMTLalpha10fewer than 2 genes could be modelled
MATscCP028774:2,096,347–2,104,342MATalphaMATALPHA10fewer than 2 genes could be modelled
MATscCP028774:2,326,639–2,326,800undeterminedMATALPHA20fewer than 2 genes could be modelled
MTLCP028774:2,525,717–2,525,908AMTLA10fewer than 2 genes could be modelled
MTLCP028774:2,723,559–2,723,657AMTLA10fewer than 2 genes could be modelled
MATscCP028776:104,762–104,863undeterminedMATALPHA20fewer than 2 genes could be modelled
MTLCP028776:157,190–157,300alphaMTLalpha10fewer than 2 genes could be modelled
MATscCP028776:199,504–199,629undeterminedMATA20fewer than 2 genes could be modelled
MTLCP028776:445,180–445,272alphaMTLalpha10fewer than 2 genes could be modelled
MATscCP028776:758,463–758,567MATalphaMATALPHA10fewer than 2 genes could be modelled
MTLCP028776:852,336–852,521AMTLA20fewer than 2 genes could be modelled
MATscCP028776:919,778–927,452MATalphaMATALPHA1, MATALPHA20fewer than 2 genes could be modelled
MTLCP028776:954,616–954,705alphaMTLalpha10fewer than 2 genes could be modelled
MATscCP028776:1,011,215–1,011,307MATalphaMATALPHA10fewer than 2 genes could be modelled
MATscCP028776:1,198,541–1,207,211undeterminedMATALPHA20fewer than 2 genes could be modelled
MATscCP028776:1,273,291–1,293,727MATalphaMATALPHA1, MATALPHA20fewer than 2 genes could be modelled
MATscCP028776:1,353,676–1,353,774undeterminedMATALPHA20fewer than 2 genes could be modelled
MATscCP028775:208,759–228,258MATalphaMATALPHA1, MATA20fewer than 2 genes could be modelled
MTLCP028775:329,875–349,022AMTLA10fewer than 2 genes could be modelled
MTLCP028775:397,652–397,786alphaMTLalpha10fewer than 2 genes could be modelled
MTLCP028775:593,480–593,593AMTLA20fewer than 2 genes could be modelled
MTLCP028775:789,560–789,688AMTLA20fewer than 2 genes could be modelled
MTLCP028775:885,261–885,461AMTLA10fewer than 2 genes could be modelled
MTLCP028775:993,275–993,463AMTLA20fewer than 2 genes could be modelled
MTLCP028775:1,023,506–1,023,814AMTLA20fewer than 2 genes could be modelled
MATscCP028775:1,248,392–1,249,105undeterminedMATA20fewer than 2 genes could be modelled
MTLCP028775:1,248,392–1,249,105AMTLA20fewer than 2 genes could be modelled
MTLCP028775:1,408,597–1,408,761AMTLA20fewer than 2 genes could be modelled
MTLCP028775:1,527,799–1,527,909alphaMTLalpha10fewer than 2 genes could be modelled
MATscCP028775:1,604,145–1,604,285undeterminedMATALPHA20fewer than 2 genes could be modelled
MATscCP028775:1,699,865–1,700,011undeterminedMATALPHA20fewer than 2 genes could be modelled
MTLCP028775:1,699,865–1,700,011AMTLA10fewer than 2 genes could be modelled
MATscCP028775:2,419,701–2,419,829MATalphaMATALPHA10fewer than 2 genes could be modelled
MTLCP028777:223,356–223,457alphaMTLalpha10fewer than 2 genes could be modelled
MTLCP028777:571,199–571,405AMTLA20fewer than 2 genes could be modelled
MTLCP028777:889,889–890,065AMTLA20fewer than 2 genes could be modelled
MTLCP028777:984,782–984,889AMTLA10fewer than 2 genes could be modelled
MTLCP028777:1,200,682–1,200,771AMTLA10fewer than 2 genes could be modelled
MTLCP028773:672,272–675,532undeterminedPIK11too few of the family's genes found
MTLCP028773:1,911,842–1,937,211undeterminedPAP1, OBP12too few of the family's genes found
MTLCP028774:1,050,574–1,053,828undeterminedPIK11too few of the family's genes found
MTLCP028774:2,096,347–2,104,342undeterminedOBP11too few of the family's genes found
MTLCP028776:1,320,146–1,325,695undeterminedPIK11too few of the family's genes found

Provenance

Genome file
PkudriavzeviiCBS573.genome.fasta
Assembly
6 contigs · 10.9 Mb · N50 2.7 Mb
Genome SHA-256
8a200fdb6d86dd69093bd58a98fcd90dfa9d47a9c5ccc29041b230d3b1cc6990
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': 'species', 'routing_taxid': 1156497, '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 1156497', 'routed_by': 'family taxid 1156497 (phylum_fallback)'}, 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
2026-11-07T02:48:48Z
Run time
27 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