MATPredict · mating-type report

TthermophilusATCC42464

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 02:35 UTC by MATPredict 0.8.1

Result

Mating type

MAT1-1high confidence

Called loci 1

MAT1-1 MAT family · Ascomycota

high confidence
Gene order of the MAT1-1 locus on CP003002MAT1-1 locus: genes from left to right on CP003002, 7,698,571 to 7,713,422: COX13 (conserved flank, minus strand); APN2 (conserved flank, plus strand); MAT1-1-3 (core MAT gene, minus strand); MAT1-2-1 (core MAT gene, minus strand); MAT1-1-2 (core MAT gene, plus strand); MAT1-1-1 (core MAT gene, plus strand); SLA2 (conserved flank, minus strand).7,700 kb7,705 kb7,710 kb3,216.9 kb more to contig end →called locusCOX13: conserved flank, 7,698,571–7,699,404 (-), identity 67.4%, search hit onlyCOX13APN2: conserved flank, 7,700,136–7,702,386 (+), identity 81.8%, search hit onlyAPN2MAT1-1-3: core MAT gene, 7,703,805–7,704,638 (-), identity 45.3%, search hit onlyMAT1-1-3MAT1-2-1: core MAT gene, 7,703,805–7,704,638 (-), identity 33.0%, search hit onlyMAT1-2-1 (lost to MAT1-1-3)MAT1-1-2: core MAT gene, 7,705,124–7,706,481 (+), identity 29.3%, search hit onlyMAT1-1-2MAT1-1-1: core MAT gene, 7,707,115–7,707,935 (+), identity 23.5%, search hit onlyMAT1-1-1SLA2: conserved flank, 7,710,010–7,713,422 (-), identity 80.4%, search hit onlySLA2
Gene order on CP003002. Scroll sideways to see the whole figure.
FungiDB release 71 gene models on CP003002, 7,697,830 to 7,714,163MYCTH_2054145 7,695,643-7,698,132 (+): Anaphase-promoting complex subunit 5 | domain-containing proteinMYCTH_2054145MYCTH_2298230 7,698,340-7,699,587 (-): Cytochrome c oxidase subunit VIa | domain-containing proteinMYCTH_2298230MYCTH_2298234 7,699,767-7,702,650 (+): DNA-(apurinic or apyrimidinic site) endonuclease 2MYCTH_2298234MYCTH_2115740 7,703,805-7,704,638 (-): HMG (high mobility group) box | domain-containing proteinMYCTH_2115740MYCTH_2107654 7,705,124-7,706,481 (+): Mating type protein 1-1-2 of unknown function | domain-containing proteinMYCTH_2107654MYCTH_2298236 7,707,055-7,707,977 (+): Mating-type protein MAT alpha 1 HMG-box | domain-containing proteinMYCTH_2298236MYCTH_2298240 7,709,772-7,713,802 (-): I/LWEQ domain | ANTH domain | domain-containing proteinMYCTH_2298240
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
  • MAT1-2-1 is a weak hit to the other idiomorph's gene and was not counted against the call.
Location
CP003002:7,698,571–7,713,422 · 14.9 kb
Own genes
CP003002:7,698,571–7,713,422 · 14.9 kb
Locus
Complete locus: MAT gene(s) with their flanking genes.
Genes modelled
6 of 7 gene hits
Nearest contig end
3.2 Mb
Region (samtools)
CP003002:7698571-7713422
Idiomorph scores
  • MAT1-1 121.0

Margin over the set-aside MAT1-2-1 hit: 12.3 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
MAT1-1-345.3MAT1-2-133.0100.0higher identity

Gene evidence

GeneRoleModel Identity %E-value Position (strand)Exons Reference recordFungiDB gene
COX13conserved flankhit onlyDIAMOND, proteome67.4cov 99.2%5.2e-65187 bits7,698,571–7,699,404 -–578113_sxlc146_MAT_MAT1-2MYCTH_2298230
APN2conserved flankhit onlyDIAMOND, proteome81.8cov 36.7%2.6e-237665 bits7,700,136–7,702,386 +–2903220_liq80xsp_MAT_combinedMYCTH_2298234
MAT1-1-3core MAThit onlyDIAMOND, proteome45.3cov 19.8%6.6e-1359 bits7,703,805–7,704,638 -–5141_74-ors-a_MAT_MAT1-1MYCTH_2115740
MAT1-2-1core MATother idiomorph, not countedlost to MAT1-1-3, not countedhit onlyDIAMOND, proteome33.0cov 35.7%9.1e-1256 bits7,703,805–7,704,638 -–578113_sxlc146_MAT_MAT1-2MYCTH_2115740
MAT1-1-2core MAThit onlyDIAMOND, proteome29.3cov 95.7%1.5e-33121 bits7,705,124–7,706,481 +–5141_74-ors-a_MAT_MAT1-1MYCTH_2107654
MAT1-1-1core MAThit onlyDIAMOND, proteome23.5cov 35.4%8.6e-0845 bits7,707,115–7,707,935 +–27337_nbrc6119_MAT_MAT1-1MYCTH_2298236
SLA2conserved flankhit onlyDIAMOND, proteome80.4cov 100.0%< 1e-1801,390 bits7,710,010–7,713,422 -–107463_unknown-1_MAT_MAT1-2MYCTH_2298240

Withheld candidate loci 4

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 (4).

Show the 4 withheld loci

Withheld loci (4)

familylocationidiomorph genesmodelledreason
MATCP003002:4,722,700–4,724,522MAT1-2MAT1-2-11too few of the family's genes found
MATCP003004:2,592,508–2,593,281MAT1-1MAT1-1-31too few of the family's genes found
MATCP003006:3,601,392–3,602,527MAT1-2MAT1-2-11too few of the family's genes found
MATCP003008:841,854–844,199MAT1-2MAT1-2-11too few of the family's genes found

Provenance

Genome file
TthermophilusATCC42464.genome.fasta
Assembly
7 contigs · 38.7 Mb · N50 5.1 Mb
Genome SHA-256
e46892427d879dfc039d6796056098508a44e939536e64dd65028bc8748d2811
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': 35718, '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 Ascomycota', 'action': 'routed', 'weak_call_accepted': False, 'genetic_code': 1, 'genetic_code_from': 'family taxid 35718', 'routed_by': 'family taxid 35718 (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, scoped_roster=off: BGL1,GAP1 not searched, supported_min_bitscore=33.0
Run started
2026-11-07T02:33:47Z
Run time
88 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