MATPredict · mating-type report

MlusitanicusCBS277-49

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 01:52 UTC by MATPredict 0.8.1

Result

Mating type

Minushigh confidence

Called loci 1

Minus MAT family · Mucoromycota

high confidence
Gene order of the Minus locus on AMYB01000005Minus locus: genes from left to right on AMYB01000005, 2,202,342 to 2,236,300: algA (variable flank, minus strand); tptA (conserved flank, minus strand); sexM (core MAT gene, plus strand); rnhA (conserved flank, plus strand); glrA (variable flank, minus strand); sexP (core MAT gene, minus strand).2,210 kb2,220 kb2,230 kb1,001.7 kb more to contig end →called locusalgA: variable flank, 2,202,342–2,203,751 (-), identity 66.9%, search hit onlyalgAtptA: conserved flank, 2,204,375–2,205,468 (-), identity 100.0%, search hit onlytptAsexM: core MAT gene, 2,206,210–2,206,959 (+), identity 100.0%, search hit onlysexMrnhA: conserved flank, 2,207,099–2,211,232 (+), identity 99.8%, search hit onlyrnhAglrA: variable flank, 2,215,764–2,217,336 (-), identity 86.5%, search hit onlyglrAsexP: core MAT gene, 2,236,058–2,236,300 (-), identity 22.222%, search hit onlysexP (lost to sexM)
Gene order on AMYB01000005. Scroll sideways to see the whole figure.
FungiDB release 68 gene models on AMYB01000005, 2,200,647 to 2,237,994MUCCIDRAFT_111720 2,202,342-2,203,751 (-): Alginate lyase domain-containing protein [Source:UniProtKB/TrEMBL;Acc:A0A168KFV4]MUCCIDRAFT_111720MUCCIDRAFT_124985 2,204,080-2,204,358 (-): Sugar phosphate transporter domain-containing protein (Fragment) [Source:UniProtKB/TrEMBL;Acc:A0A168KFW5]MUCCIDRAFT_124985MUCCIDRAFT_145196 2,204,375-2,205,468 (-): Sugar phosphate transporter domain-containing protein [Source:UniProtKB/TrEMBL;Acc:A0A162QIM5]MUCCIDRAFT_145196MUCCIDRAFT_153347 2,206,210-2,206,959 (+): HMG box domain-containing protein [Source:UniProtKB/TrEMBL;Acc:A0A168KFX3]MUCCIDRAFT_153347MUCCIDRAFT_143979 2,207,099-2,211,232 (+): RNA helicase [Source:UniProtKB/TrEMBL;Acc:A0A162T6S6]MUCCIDRAFT_143979MUCCIDRAFT_82733 2,213,093-2,215,666 (+): Fungal-specific transcription factor [Source:UniProtKB/TrEMBL;Acc:A0A168KFX6]MUCCIDRAFT_82733MUCCIDRAFT_184608 2,215,673-2,217,336 (-): NDE4MUCCIDRAFT_184608 NDE4MUCCIDRAFT_t136 2,218,750-2,218,821 (+): tRNA-GluMUCCIDRAFT_t136MUCCIDRAFT_111726 2,221,757-2,222,455 (-): unspecified productMUCCIDRAFT_111726MUCCIDRAFT_111728 2,224,908-2,226,009 (-): No apical meristem-associated C-terminal domain-containing protein [Source:UniProtKB/TrEMBL;Acc:A0A168KG11]MUCCIDRAFT_111728MUCCIDRAFT_164283 2,233,315-2,235,720 (-): Reverse transcriptase domain-containing protein [Source:UniProtKB/TrEMBL;Acc:A0A168KG23]MUCCIDRAFT_164283
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
  • conserved flank
  • variable flank
  • search hit only
  • sexP is a weak hit to the other idiomorph's gene and was not counted against the call.
Location
AMYB01000005:2,202,342–2,236,300 · 34.0 kb
Own genes
AMYB01000005:2,202,342–2,236,300 · 34.0 kb
Locus
Complete locus: MAT gene(s) with their flanking genes.
Genes modelled
5 of 6 gene hits
Nearest contig end
1.0 Mb
Region (samtools)
AMYB01000005:2202342-2236300
Idiomorph scores
  • Minus 114.6
  • Plus 36.0

Margin over the next idiomorph: 78.6

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

Profile-HMM classifier
  • Minus 114.6
  • Plus 36.0

Margin 78.6 (a call needs 25.0 or more). Scored: sexP, sexP, sexP, sexP (hit fragment).

Overlapping hits resolved

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

keptidentity %set asideidentity %overlap %basis
sexM100.0sexP32.9100.0higher identity

Gene evidence

GeneRoleModel Identity %E-value Position (strand)Exons Reference recordFungiDB gene
algAvariable flankhit onlyDIAMOND, proteome66.9cov 99.2%1.4e-194535 bits2,202,342–2,203,751 -–29922_cbs109-16_MAT_MinusMUCCIDRAFT_111720
tptAconserved flankhit onlyDIAMOND, proteome100.0cov 100.0%9.9e-199536 bits2,204,375–2,205,468 -–36080_nrrl-3631_MAT_PlusMUCCIDRAFT_145196
sexMcore MAThit onlyDIAMOND, proteome100.0cov 100.0%4.0e-180487 bits2,206,210–2,206,959 +–36080_r7b_MAT_MinusMUCCIDRAFT_153347
rnhAconserved flankhit onlyDIAMOND, proteome99.8cov 100.0%< 1e-1802,395 bits2,207,099–2,211,232 +–36080_r7b_MAT_MinusMUCCIDRAFT_143979
glrAvariable flankhit onlyDIAMOND, proteome86.5cov 100.0%6.7e-304818 bits2,215,764–2,217,336 -–3108396_ai-2023a_MAT_PlusMUCCIDRAFT_184608 NDE4
sexPcore MATother idiomorph, not countedlost to sexM, not countedhit onlytblastn22.2cov 24.0%5.4e+0029 bits2,236,058–2,236,300 -–101119_atcc11807_MAT_Plusnone

Withheld candidate loci 13

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 (12); fewer than 2 genes could be modelled (1).

Show the 13 withheld loci

Withheld loci (13)

familylocationidiomorph genesmodelledreason
MATAMYB01000002:4,574,804–4,581,202undeterminedsexP, sexM, glrA1fewer than 2 genes could be modelled
MATAMYB01000001:3,125,369–3,126,757undeterminedtptA1too few of the family's genes found
MATAMYB01000002:36,861–37,653undeterminedbtbA1too few of the family's genes found
MATAMYB01000002:1,188,686–1,189,848undeterminedtptA1too few of the family's genes found
MATAMYB01000002:3,758,038–3,762,619undeterminedrnhA1too few of the family's genes found
MATAMYB01000003:704,146–704,743undeterminedsexM1too few of the family's genes found
MATAMYB01000003:886,845–888,669undeterminedglrA1too few of the family's genes found
MATAMYB01000003:2,539,519–2,541,298undeterminedrnhA1too few of the family's genes found
MATAMYB01000004:609,434–610,557undeterminedtptA1too few of the family's genes found
MATAMYB01000004:1,621,809–1,694,175undeterminedtptA, sexP1too few of the family's genes found
MATAMYB01000004:2,044,703–2,048,603undeterminedrnhA1too few of the family's genes found
MATAMYB01000014:85,211–88,629undeterminedrnhA1too few of the family's genes found
MATAMYB01000016:29,952–31,482undeterminedglrA1too few of the family's genes found

Provenance

Genome file
MlusitanicusCBS277-49.genome.fasta
Assembly
21 contigs · 36.6 Mb · N50 4.3 Mb
Genome SHA-256
6a82eff53ae05c05df80d321522ec2b81810627229b0a9c865fee0547fc36bfe
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': 34489, '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 34489', 'routed_by': 'family taxid 34489 (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
2026-11-07T01:51:24Z
Run time
53 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