MATPredict · mating-type report

RdelemarRA99-880

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 02:47 UTC by MATPredict 0.8.1

Result

Mating type

Plushigh confidence

Called loci 1

Plus MAT family · Mucoromycota

high confidence
Gene order of the Plus locus on CH476732Plus locus: genes from left to right on CH476732, 3,251,438 to 3,316,651: btbA (variable flank, plus strand); sexP (core MAT gene, plus strand); sexM (core MAT gene, plus strand); rnhA (conserved flank, plus strand); glrA (variable flank, minus strand).3,260 kb3,280 kb3,300 kb2,415.6 kb more to contig end →called locusbtbA: variable flank, 3,305,306–3,307,136 (+), identity 90.7%, search hit onlybtbAsexP: core MAT gene, 3,309,519–3,310,457 (+), identity 93.29%, gene modelsexPsexM: core MAT gene, 3,309,861–3,310,079 (+), identity 28.77%, gene modelsexM (lost to sexP)rnhA: conserved flank, 3,310,529–3,314,719 (+), identity 88.2%, search hit onlyrnhAglrA: variable flank, 3,315,053–3,316,651 (-), identity 84.0%, search hit onlyglrA
Gene order on CH476732. Scroll sideways to see the whole figure.
FungiDB release 71 gene models on CH476732, 3,248,177 to 3,319,909RO3G_01270 3,248,287-3,248,877 (+): hypothetical proteinRO3G_01270RO3G_01271 3,249,612-3,250,947 (-): LIM domain | domain-containing proteinRO3G_01271RO3G_01272 3,251,438-3,257,236 (-): Helicase SEN1 beta-barrel domain | AAA domain | AAA domain | SEN1 N terminal | domain-containing proteinRO3G_01272RO3G_01273 3,258,582-3,258,781 (-): hypothetical proteinRO3G_01273RO3G_01274 3,261,122-3,262,273 (+): hypothetical proteinRO3G_01274RO3G_01275 3,263,700-3,265,066 (+): ATP-dependent Clp protease, ATP-binding subunit ClpXRO3G_01275RO3G_01276 3,265,412-3,267,793 (+): SWIB/MDM2 domain | domain-containing proteinRO3G_01276RO3G_01277 3,268,617-3,268,988 (+): hypothetical proteinRO3G_01277RO3G_01278 3,269,672-3,270,230 (-): rhizopuspepsinRO3G_01278RO3G_01279 3,270,544-3,270,996 (-): hypothetical proteinRO3G_01279RO3G_01280 3,272,485-3,273,433 (+): prohibitin-1RO3G_01280RO3G_19014 3,278,209-3,278,280 (-): tRNA-GluRO3G_19014RO3G_01281 3,282,636-3,282,902 (+): hypothetical proteinRO3G_01281RO3G_01282 3,283,909-3,285,014 (+): RhizopuspepsinRO3G_01282RO3G_01283 3,288,551-3,289,649 (-): Alcohol dehydrogenase GroES-like domain | Zinc-binding dehydrogenase | domain-containing proteinRO3G_01283RO3G_01284 3,291,838-3,292,579 (+): 3,4-dihydroxy-2-butanone 4-phosphate synthaseRO3G_01284RO3G_01285 3,292,826-3,294,515 (+): ATP synthase subunit betaRO3G_01285RO3G_01286 3,294,641-3,295,459 (+): hypothetical proteinRO3G_01286RO3G_01287 3,295,901-3,296,140 (-): hypothetical proteinRO3G_01287RO3G_01288 3,303,487-3,304,968 (+): Regulator of chromosome condensation (RCC1) repeat | Ankyrin repeats (3 copies) | domain-containing proteinRO3G_01288RO3G_01289 3,305,306-3,307,136 (+): BTB/POZ domain | domain-containing proteinRO3G_01289RO3G_01290 3,307,465-3,308,089 (+): hypothetical proteinRO3G_01290RO3G_01291 3,310,529-3,314,719 (+): AAA domain | AAA domain | ZNFX1 domain | domain-containing proteinRO3G_01291RO3G_01292 3,315,053-3,316,651 (-): glutathione-disulfide reductaseRO3G_01292RO3G_01293 3,317,309-3,317,599 (+): hypothetical proteinRO3G_01293RO3G_01294 3,318,741-3,320,828 (-): Reverse transcriptase (RNA-dependent DNA polymerase) | domain-containing proteinRO3G_01294
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
  • variable flank
  • gene model
  • search hit only
  • sexM is a weak hit to the other idiomorph's gene and was not counted against the call.
Location
CH476732:3,251,438–3,316,651 · 65.2 kb
Own genes
CH476732:3,305,306–3,316,651 · 11.3 kb · the span runs 53.9 kb beyond these genes
Locus
Complete locus: MAT gene(s) with their flanking genes.
Genes modelled
4 of 5 gene hits
Nearest contig end
2.4 Mb
Region (samtools)
CH476732:3251438-3316651
Idiomorph scores
  • Plus 359.5
  • Minus 50.9

Margin over the next idiomorph: 308.6

Score: HMM bitscore of the MAT protein against each idiomorph's profile.

Profile-HMM classifier
  • Minus 50.9
  • Plus 359.5

Margin 308.6 (a call needs 25.0 or more). Scored: sexP, sexP (model).

Overlapping hits resolved

Where genes of two idiomorphs hit the same place, the stronger hit was kept.

keptidentity %set asideidentity %overlap %basis
sexP93.3sexM28.8100.0profile bitscore of its own idiomorph

Gene evidence

GeneRoleModel Identity %E-value Position (strand)Exons Reference recordFungiDB gene
btbAvariable flankhit onlyDIAMOND, proteome90.7cov 56.5%< 1e-180995 bits3,305,306–3,307,136 +–64495_cbs346-36_MAT_PlusRO3G_01289
sexPcore MATgene modelexonerate93.3cov 100.0%< 1e-180595 bits3,309,519–3,310,457 +164495_cbs346-36_MAT_Plusnone
sexMcore MATother idiomorph, not countedlost to sexP, not countedgene modelexonerate28.8cov 34.6%7.1e+0028 bits3,309,861–3,310,079 +14837_nrrl1555_MAT_Minusnone
rnhAconserved flankhit onlyDIAMOND, proteome88.2cov 100.0%< 1e-1801,951 bits3,310,529–3,314,719 +–64495_cbs110-17_MAT_MinusRO3G_01291
glrAvariable flankhit onlyDIAMOND, proteome84.0cov 100.0%3.9e-281759 bits3,315,053–3,316,651 -–86630_cbs357-93_MAT_MinusRO3G_01292
tptAexpected, not found–
algAexpected, not found–

Withheld candidate loci 14

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 (14).

Show the 14 withheld loci

Withheld loci (14)

familylocationidiomorph genesmodelledreason
MATCH476732:56,695–58,163undeterminedglrA1too few of the family's genes found
MATCH476732:2,676,920–2,677,792undeterminedtptA1too few of the family's genes found
MATCH476733:2,763,140–2,766,604undeterminedrnhA1too few of the family's genes found
MATCH476734:1,649,744–1,650,767undeterminedtptA1too few of the family's genes found
MATCH476735:2,113,486–2,114,022undeterminedtptA1too few of the family's genes found
MATCH476739:588,686–650,868undeterminedsexM, glrA2too few of the family's genes found
MATCH476739:1,493,176–1,496,765undeterminedglrA1too few of the family's genes found
MATCH476739:1,737,817–1,743,327undeterminedrnhA1too few of the family's genes found
MATCH476739:2,142,172–2,145,937undeterminedrnhA1too few of the family's genes found
MATCH476740:97,666–98,620undeterminedtptA1too few of the family's genes found
MATCH476742:499,764–500,675undeterminedsexM1too few of the family's genes found
MATCH476744:738,609–740,966undeterminedrnhA1too few of the family's genes found
MATCH476746:51,115–63,365undeterminedsexM, algA1too few of the family's genes found
MATCH476749:358,280–360,107undeterminedglrA1too few of the family's genes found

Provenance

Genome file
RdelemarRA99-880.genome.fasta
Assembly
83 contigs · 46.1 Mb · N50 3.1 Mb
Genome SHA-256
0a50344f3e6e4297820a1bc602362cc068ef9aa66a2d7851b9aec13a1e5bb8c8
MATPredict
0.8.1 (v0.8.1, 3a62e6302b)
Database
86f18d232e4fe95d · 185 records
Taxonomy
local NCBI taxonomy snapshot 2026-10-01
Parameters
phylum=Mucoromycota, phylum_guess={'requested': 'auto', 'status': 'ok', 'usable': True, 'reason': None, 'phylum': 'Mucoromycota', 'phylum_taxid': 1913637, 'deepest_rank': 'species', 'routing_taxid': 1344955, '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 Mucoromycota', 'action': 'routed', 'weak_call_accepted': False, 'genetic_code': 1, 'genetic_code_from': 'family taxid 1344955', 'routed_by': 'family taxid 1344955 (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
2026-11-07T02:46:46Z
Run time
55 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