MATPredict · mating-type report

KlactisNRRLY-1140

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 02:45 UTC by MATPredict 0.8.1

Result

Mating-type loci

MATahigh confidenceMATalphahigh confidenceMATahigh confidence

Called loci 3

MATa MATsc family · Ascomycota

high confidence
Gene order of the MATa locus on CR382122MATa locus: genes from left to right on CR382122, 1,278,225 to 1,280,936: sla2 (conserved flank, plus strand); MATA1 (core MAT gene, minus strand); MATA2 (core MAT gene, plus strand).1,278.0 kb1,278.5 kb1,279.0 kb1,279.5 kb1,280.0 kb1,280.5 kb1,281.0 kb39.6 kb more to contig end →called locussla2: conserved flank, 1,278,225–1,278,557 (+), identity 100.0%, search hit onlysla2MATA1: core MAT gene, 1,278,622–1,279,308 (-), identity 100.0%, search hit onlyMATA1MATA2: core MAT gene, 1,280,163–1,280,936 (+), identity 100.0%, search hit onlyMATA2
Gene order on CR382122. Scroll sideways to see the whole figure.
FungiDB release 71 gene models on CR382122, 1,277,925 to 1,281,236KLLA0_B14531g 1,278,225-1,278,557 (+): unspecified productKLLA0_B14531gKLLA0_B14553g 1,278,622-1,279,308 (-): Homeodomain | domain-containing proteinKLLA0_B14553gKLLA0_B14575g 1,280,163-1,280,936 (+): unspecified productKLLA0_B14575g
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
Location
CR382122:1,278,225–1,280,936 · 2.7 kb
Cross-lineage class
MAT1-2
Own genes
CR382122:1,278,225–1,280,936 · 2.7 kb
Locus
Complete locus: MAT gene(s) with their flanking genes.
Genes modelled
3 of 3 gene hits
Nearest contig end
39.9 kb
Region (samtools)
CR382122:1278225-1280936
Idiomorph scores
  • MATa 456.0

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
sla2conserved flankhit onlyDIAMOND, proteome100.0cov 16.4%1.3e-69210 bits1,278,225–1,278,557 +–28985_nrrl-y-1140_MATsc_MATaKLLA0_B14531g
MATA1core MAThit onlyDIAMOND, proteome100.0cov 100.0%1.8e-169456 bits1,278,622–1,279,308 -–28985_nrrl-y-1140_MATsc_MATaKLLA0_B14553g
MATA2core MAThit onlyDIAMOND, proteome100.0cov 100.0%2.5e-156425 bits1,280,163–1,280,936 +–28985_nrrl-y-1140_MATsc_MATaKLLA0_B14575g
cha1not searchable: no reference protein in the database–

MATalpha MATsc family · Ascomycota

high confidence
Gene order of the MATalpha locus on CR382123MATalpha locus: genes from left to right on CR382123, 23,718 to 25,803: sla2 (conserved flank, plus strand); MATALPHA1 (core MAT gene, minus strand); MATA2 (core MAT gene, plus strand); MATALPHA2 (core MAT gene, plus strand).23.5 kb24.0 kb24.5 kb25.0 kb25.5 kb26.0 kb← 23.4 kb more to contig endcalled locussla2: conserved flank, 23,718–24,050 (+), identity 100.0%, search hit onlysla2MATALPHA1: core MAT gene, 24,124–24,909 (-), identity 100.0%, search hit onlyMATALPHA1MATA2: core MAT gene, 25,132–25,803 (+), identity 35.4%, search hit onlyMATA2 (lost to MATALPHA2)MATALPHA2: core MAT gene, 25,132–25,803 (+), identity 100.0%, search hit onlyMATALPHA2
Gene order on CR382123. Scroll sideways to see the whole figure.
FungiDB release 71 gene models on CR382123, 23,418 to 26,103KLLA0_C00330g 23,718-24,050 (+): unspecified productKLLA0_C00330gKLLA0_C00352g 24,124-24,909 (-): Mating-type protein MAT alpha 1 HMG-box | domain-containing proteinKLLA0_C00352gKLLA0_C00374g 25,132-25,803 (+): Homeobox KN domain | domain-containing proteinKLLA0_C00374g
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
  • MATA2 is a weak hit to the other idiomorph's gene and was not counted against the call.
Location
CR382123:23,718–25,803 · 2.1 kb
Cross-lineage class
MAT1-1
Own genes
CR382123:23,718–25,803 · 2.1 kb
Locus
Complete locus: MAT gene(s) with their flanking genes.
Genes modelled
3 of 4 gene hits
Nearest contig end
23.7 kb
Region (samtools)
CR382123:23718-25803
Idiomorph scores
  • MATalpha 514.0

Margin over the set-aside MATA2 hit: 64.6 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
MATALPHA2100.0MATA235.4100.0higher identity

Gene evidence

GeneRoleModel Identity %E-value Position (strand)Exons Reference recordFungiDB gene
sla2conserved flankhit onlyDIAMOND, proteome100.0cov 16.4%1.3e-69210 bits23,718–24,050 +–28985_nrrl-y-1140_MATsc_MATaKLLA0_C00330g
MATALPHA1core MAThit onlyDIAMOND, proteome100.0cov 100.0%2.1e-191514 bits24,124–24,909 -–28985_nrrl-y-1140_MATsc_HMLalphaKLLA0_C00352g
MATA2core MATother idiomorph, not countedlost to MATALPHA2, not countedhit onlyDIAMOND, proteome35.4cov 79.8%9.4e-2174 bits25,132–25,803 +–4932_s288c_MATsc_HMRaKLLA0_C00374g
MATALPHA2core MAThit onlyDIAMOND, proteome100.0cov 100.0%2.3e-158427 bits25,132–25,803 +–28985_nrrl-y-1140_MATsc_HMLalphaKLLA0_C00374g
cha1not searchable: no reference protein in the database–

MATa MATsc family · Ascomycota

high confidence
Gene order of the MATa locus on CR382123MATa locus: genes from left to right on CR382123, 277,789 to 282,183: sla2 (conserved flank, plus strand); MATA1 (core MAT gene, minus strand); MATA2 (core MAT gene, plus strand).278 kb279 kb280 kb281 kb282 kb← 277.5 kb more to contig endcalled locussla2: conserved flank, 277,789–279,804 (+), identity 100.0%, search hit onlysla2MATA1: core MAT gene, 279,869–280,555 (-), identity 100.0%, search hit onlyMATA1MATA2: core MAT gene, 281,410–282,183 (+), identity 100.0%, search hit onlyMATA2
Gene order on CR382123. Scroll sideways to see the whole figure.
FungiDB release 71 gene models on CR382123, 277,489 to 282,483KLLA0_C03113g 277,789-279,804 (+): ANTH domain | domain-containing proteinKLLA0_C03113gKLLA0_C03135g 279,869-280,555 (-): Homeodomain | domain-containing proteinKLLA0_C03135gKLLA0_C03157g 281,410-282,183 (+): unspecified productKLLA0_C03157gKLLA0_C03179g 282,251-286,687 (-): Laa1/Sip1/HEATR5 HEAT repeat region | domain-containing proteinKLLA0_C03179g
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
Location
CR382123:277,789–282,183 · 4.4 kb
Cross-lineage class
MAT1-2
Own genes
CR382123:277,789–282,183 · 4.4 kb
Locus
Complete locus: MAT gene(s) with their flanking genes.
Genes modelled
3 of 3 gene hits
Nearest contig end
277.8 kb
Region (samtools)
CR382123:277789-282183
Idiomorph scores
  • MATa 456.0

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
sla2conserved flankhit onlyDIAMOND, proteome100.0cov 100.0%< 1e-1801,206 bits277,789–279,804 +–28985_nrrl-y-1140_MATsc_MATaKLLA0_C03113g
MATA1core MAThit onlyDIAMOND, proteome100.0cov 100.0%1.8e-169456 bits279,869–280,555 -–28985_nrrl-y-1140_MATsc_MATaKLLA0_C03135g
MATA2core MAThit onlyDIAMOND, proteome100.0cov 100.0%2.5e-156425 bits281,410–282,183 +–28985_nrrl-y-1140_MATsc_MATaKLLA0_C03157g
cha1not searchable: no reference protein in the database–

Withheld candidate loci 18

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 (18).

Show the 18 withheld loci

Withheld loci (18)

familylocationidiomorph genesmodelledreason
MATscCR382122:125,621–125,800undeterminedMATALPHA20fewer than 2 genes could be modelled
MATscCR382122:913,642–913,797undeterminedMATALPHA20fewer than 2 genes could be modelled
MATscCR382122:1,233,930–1,234,019undeterminedMATALPHA20fewer than 2 genes could be modelled
MATscCR382126:157,779–157,934MATalphaMATALPHA10fewer than 2 genes could be modelled
MATscCR382126:281,244–281,390undeterminedMATALPHA20fewer than 2 genes could be modelled
MATscCR382126:469,379–469,576undeterminedMATALPHA20fewer than 2 genes could be modelled
MATscCR382126:1,783,344–1,783,490MATalphaMATALPHA10fewer than 2 genes could be modelled
MATscCR382126:2,080,264–2,080,458MATalphaMATALPHA10fewer than 2 genes could be modelled
MATscCR382125:24,438–24,530undeterminedMATALPHA20fewer than 2 genes could be modelled
MATscCR382125:477,038–477,307undeterminedMATALPHA20fewer than 2 genes could be modelled
MATscCR382125:664,952–665,122MATalphaMATALPHA10fewer than 2 genes could be modelled
MATscCR382125:695,802–695,957undeterminedMATALPHA20fewer than 2 genes could be modelled
MATscCR382125:1,443,177–1,443,368MATaMATA10fewer than 2 genes could be modelled
MATscCR382125:1,562,792–1,563,220MATalphaMATALPHA10fewer than 2 genes could be modelled
MATscCR382124:849,849–850,010MATaMATA10fewer than 2 genes could be modelled
MATscCR382124:1,065,373–1,065,522undeterminedMATALPHA20fewer than 2 genes could be modelled
MATscCR382121:522,010–522,294undeterminedMATALPHA20fewer than 2 genes could be modelled
MATscCR382121:656,890–657,165MATalphaMATALPHA10fewer than 2 genes could be modelled

Provenance

Genome file
KlactisNRRLY-1140.genome.fasta
Assembly
6 contigs · 10.7 Mb · N50 1.8 Mb
Genome SHA-256
6388de0d9426be3a352f9c01933408bd8eb49664b89b62d633f7e381fac162ff
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': 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
2026-11-07T02:45:05Z
Run time
13 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