MATPredict · mating-type report

LtigrinusALCF2SS1-7

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 02:11 UTC by MATPredict 0.8.1

Result

Mating-type loci

undeterminedHDhigh confidenceundeterminedPRmedium confidence

Called loci 2

undetermined HD family · Basidiomycota

high confidence
Gene order of the undetermined locus on ML122043undetermined locus: genes from left to right on ML122043, 2,158,054 to 2,166,246: MIP1 (conserved flank, plus strand); HD2 (core MAT gene, minus strand); HD1 (core MAT gene, plus strand); beta_fg (conserved flank, minus strand).2,158 kb2,160 kb2,162 kb2,164 kb2,166 kb1,370.1 kb more to contig end →called locusMIP1: conserved flank, 2,158,054–2,160,530 (+), identity 79.8%, search hit onlyMIP1HD2: core MAT gene, 2,161,348–2,161,587 (-), identity 41.77%, gene modelHD2HD1: core MAT gene, 2,162,791–2,163,081 (+), identity 32.63%, gene modelHD1beta_fg: conserved flank, 2,165,286–2,166,246 (-), identity 61.9%, search hit onlybeta_fg
Gene order on ML122043. Scroll sideways to see the whole figure.
FungiDB release 68 gene models on ML122043, 2,157,645 to 2,166,655L226DRAFT_528548 2,155,356-2,157,881 (+): WHIM1 domain-containing protein [Source:UniProtKB/TrEMBL;Acc:A0A5C2U1I1]L226DRAFT_528548L226DRAFT_549213 2,158,037-2,160,611 (+): mitochondrial intermediate peptidaseL226DRAFT_549213L226DRAFT_24541 2,160,638-2,161,823 (-): unspecified productL226DRAFT_24541L226DRAFT_24547 2,161,736-2,162,605 (-): unspecified productL226DRAFT_24547L226DRAFT_564962 2,162,779-2,164,307 (+): Mating-type protein A-alpha/beta 1 N-terminal domain-containing protein [Source:UniProtKB/TrEMBL;Acc:A0A5C2TZ14]L226DRAFT_564962L226DRAFT_607515 2,165,147-2,166,246 (-): Beta-flanking protein [Source:UniProtKB/TrEMBL;Acc:A0A5C2UBG3]L226DRAFT_607515L226DRAFT_528552 2,166,562-2,169,075 (+): MFS polyamine transporterL226DRAFT_528552
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
  • gene model
  • search hit only
  • Idiomorph undetermined: the evidence for two idiomorphs is tied or too close to call.
Location
ML122043:2,158,054–2,166,246 · 8.2 kb
Own genes
ML122043:2,158,054–2,166,246 · 8.2 kb
Locus
Complete locus: MAT gene(s) with their flanking genes.
Genes modelled
4 of 4 gene hits
Nearest contig end
1.4 Mb
Region (samtools)
ML122043:2158054-2166246

Gene evidence

GeneRoleModel Identity %E-value Position (strand)Exons Reference recordFungiDB gene
MIP1conserved flankhit onlyDIAMOND, proteome79.8cov 99.2%< 1e-180964 bits2,158,054–2,160,530 +–2822231_sb25_HD_A1L226DRAFT_549213
HD2core MATgene modelexonerate41.8cov 15.7%2.1e-0960 bits2,161,348–2,161,587 -12822231_sb25_HD_A1L226DRAFT_24541
HD1core MATgene modelexonerate32.6cov 15.0%1.6e-0755 bits2,162,791–2,163,081 +12822231_sb25_HD_A1L226DRAFT_564962
beta_fgconserved flankhit onlyDIAMOND, proteome61.9cov 98.2%3.5e-77224 bits2,165,286–2,166,246 -–192523_h97_HD_A1L226DRAFT_607515

undetermined PR family · Basidiomycota

medium confidence
Gene order of the undetermined locus on ML122049undetermined locus: genes from left to right on ML122049, 412,981 to 460,156: pheromone_receptor (core MAT gene, minus strand); caax_precursor (core MAT gene, plus strand); pheromone_B43 (core MAT gene, minus strand); fungal_mating_type_pheromone (core MAT gene, plus strand).420 kb430 kb440 kb450 kb460 kb← 410.6 kb more to contig endcalled locuspheromone_receptor: core MAT gene, 442,380–443,637 (-), identity 73.3%, search hit onlypheromone_receptorcaax_precursor: core MAT gene, 444,177–444,341 (+), identity 0.0%, search hit onlycaax_precursorpheromone_B43: core MAT gene, 457,867–457,977 (-), identity 35.714%, search hit onlypheromone_B43fungal_mating_type_pheromone: core MAT gene, 460,025–460,153 (+), identity 56.522%, search hit onlyfungal_mating_type_pheromone
Gene order on ML122049. Scroll sideways to see the whole figure.
FungiDB release 68 gene models on ML122049, 410,620 to 462,514L226DRAFT_532935 410,386-410,826 (-): unspecified productL226DRAFT_532935L226DRAFT_602096 412,785-414,570 (-): STE3-domain-containing proteinL226DRAFT_602096L226DRAFT_611328 416,793-418,259 (+): MYND-type domain-containing protein [Source:UniProtKB/TrEMBL;Acc:A0A5C2TL49]L226DRAFT_611328L226DRAFT_551798 419,605-420,872 (+): MYND-type domain-containing protein [Source:UniProtKB/TrEMBL;Acc:A0A5C2TI98]L226DRAFT_551798L226DRAFT_569157 422,603-424,479 (+): STE3-domain-containing proteinL226DRAFT_569157L226DRAFT_459267 425,110-426,666 (+): unspecified productL226DRAFT_459267L226DRAFT_354773 426,807-427,853 (+): unspecified productL226DRAFT_354773L226DRAFT_569159 427,939-429,732 (-): unspecified productL226DRAFT_569159L226DRAFT_569160 430,740-431,489 (-): unspecified productL226DRAFT_569160L226DRAFT_354808 431,397-432,356 (-): unspecified productL226DRAFT_354808L226DRAFT_611334 432,795-434,527 (+): F-box domain-containing protein [Source:UniProtKB/TrEMBL;Acc:A0A5C2TKE9]L226DRAFT_611334L226DRAFT_433016 435,301-435,633 (-): unspecified productL226DRAFT_433016L226DRAFT_459935 437,933-439,301 (+): MYND-type domain-containing protein [Source:UniProtKB/TrEMBL;Acc:A0A5C2TL59]L226DRAFT_459935L226DRAFT_483158 442,335-443,774 (-): fungal pheromone STE3G-protein-coupled receptorL226DRAFT_483158L226DRAFT_532945 443,919-444,693 (+): Pheromone [Source:UniProtKB/TrEMBL;Acc:A0A5C2TLW7]L226DRAFT_532945L226DRAFT_354894 445,675-446,576 (+): unspecified productL226DRAFT_354894L226DRAFT_504853 448,088-450,409 (-): STE3-domain-containing proteinL226DRAFT_504853L226DRAFT_569167 451,340-451,631 (-): Fungal-type protein kinase domain-containing protein [Source:UniProtKB/TrEMBL;Acc:A0A5C2TP87]L226DRAFT_569167L226DRAFT_354987 453,157-454,173 (-): unspecified productL226DRAFT_354987L226DRAFT_559134 454,542-456,845 (-): STE3-domain-containing proteinL226DRAFT_559134L226DRAFT_532953 457,852-458,121 (-): Pheromone [Source:UniProtKB/TrEMBL;Acc:A0A5C2TKF8]L226DRAFT_532953L226DRAFT_355066 459,142-460,465 (+): unspecified productL226DRAFT_355066L226DRAFT_355148 461,623-463,392 (+): F-box domain-containing protein [Source:UniProtKB/TrEMBL;Acc:A0A5C2TL69]L226DRAFT_355148
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
  • search hit only
  • The pheromone-precursor gene was found only by a sequence-motif scan (CAAX), with no reference match. Treat this call as unconfirmed.
  • Idiomorph undetermined: the evidence for two idiomorphs is tied or too close to call.
  • Part of pheromone-receptor array Basidiomycota:PR:ML122049:412981-456736 (5 loci, supported). Arrays hold mating and non-mating receptors, so membership is not evidence of mating function.
Location
ML122049:412,981–460,156 · 47.2 kb
Own genes
ML122049:442,380–460,153 · 17.8 kb · the span runs 29.4 kb beyond these genes
Supported span
ML122049:412,981–460,153 · 47.2 kb · 3 bp of the reported span rests only on hits below 33 bits
Locus
A MAT gene with no flanking gene beside it; not a full locus.
Genes modelled
2 of 4 gene hits
Nearest contig end
413.0 kb
Region (samtools)
ML122049:412981-460156

Gene evidence

GeneRoleModel Identity %E-value Position (strand)Exons Reference recordFungiDB gene
pheromone_receptorcore MAThit onlyDIAMOND, proteome73.3cov 98.4%1.2e-184516 bits442,380–443,637 -–5627_9006-11_PR_B1L226DRAFT_483158
caax_precursorcore MATcaax orfmotif scan (CAAX)motif CVIA, 54 aa ORF0.0–444,177–444,341 +–caax_scan:CVIAL226DRAFT_532945
pheromone_B43core MAThit onlytblastn35.7cov 66.0%3.5e+0025 bits457,867–457,977 -–5346_a43-b43-okayama-7_PR_B43L226DRAFT_532953
fungal_mating_type_pheromonecore MAThit onlytblastn56.5cov 100.0%7.0e-0846 bits460,025–460,153 +–5325_fp-101664-ss1_PR_B1L226DRAFT_355066
pheromone_B44expected, not found–

Withheld candidate loci 75

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 (72); too few of the family's genes found (3).

Show the 75 withheld loci

Withheld loci (75)

familylocationidiomorph genesmodelledreason
HDML122043:1,313,982–1,314,188undeterminedHD20fewer than 2 genes could be modelled
HDML122043:1,858,859–1,859,122undeterminedHD20fewer than 2 genes could be modelled
HDML122043:2,100,860–2,102,357undeterminedHD21fewer than 2 genes could be modelled
HDML122043:2,334,658–2,334,891undeterminedHD10fewer than 2 genes could be modelled
HDML122043:3,504,861–3,505,253undeterminedHD10fewer than 2 genes could be modelled
HDML122047:250,147–250,332undeterminedHD20fewer than 2 genes could be modelled
HDML122047:369,062–396,002undeterminedHD1, HD21fewer than 2 genes could be modelled
HDML122047:424,892–440,999undeterminedHD10fewer than 2 genes could be modelled
HDML122049:39,605–39,754undeterminedHD20fewer than 2 genes could be modelled
HDML122049:65,687–65,836undeterminedHD20fewer than 2 genes could be modelled
HDML122049:330,713–331,030undeterminedHD10fewer than 2 genes could be modelled
HDML122049:675,520–680,440undeterminedHD20fewer than 2 genes could be modelled
HDML122049:918,185–918,361undeterminedHD20fewer than 2 genes could be modelled
PRML122049:1,277,809–1,284,109undeterminedpheromone_receptor, fungal_mating_type_pheromone0fewer than 2 genes could be modelled
HDML122049:1,324,700–1,347,812undeterminedHD20fewer than 2 genes could be modelled
HDML122068:401,949–402,125undeterminedHD1, HD20fewer than 2 genes could be modelled
HDML122073:65,183–70,785undeterminedHD20fewer than 2 genes could be modelled
HDML122055:9,770–13,008undeterminedHD10fewer than 2 genes could be modelled
HDML122055:85,548–85,709undeterminedHD20fewer than 2 genes could be modelled
HDML122055:541,029–544,051undeterminedHD1, HD20fewer than 2 genes could be modelled
HDML122108:59,493–59,585undeterminedHD20fewer than 2 genes could be modelled
HDML122066:34,731–34,877undeterminedHD20fewer than 2 genes could be modelled
HDML122056:298,233–298,427undeterminedHD10fewer than 2 genes could be modelled
HDML122056:479,047–479,181undeterminedHD20fewer than 2 genes could be modelled
HDML122056:538,304–538,513undeterminedHD20fewer than 2 genes could be modelled
HDML122057:272,585–272,725undeterminedHD1, HD20fewer than 2 genes could be modelled
HDML122087:107,226–109,144undeterminedHD20fewer than 2 genes could be modelled
HDML122087:156,133–172,208undeterminedHD20fewer than 2 genes could be modelled
HDML122060:117,671–133,049undeterminedHD20fewer than 2 genes could be modelled
HDML122060:468,972–491,539undeterminedHD20fewer than 2 genes could be modelled
HDML122089:67,724–67,909undeterminedHD10fewer than 2 genes could be modelled
PRML122044:472,026–503,153undeterminedpheromone_receptor, fungal_mating_type_pheromone0fewer than 2 genes could be modelled
HDML122044:1,058,620–1,058,781undeterminedHD10fewer than 2 genes could be modelled
HDML122044:1,329,819–1,341,794undeterminedHD20fewer than 2 genes could be modelled
HDML122044:1,546,421–1,546,648undeterminedHD20fewer than 2 genes could be modelled
HDML122044:1,924,032–1,924,247undeterminedHD10fewer than 2 genes could be modelled
HDML122069:247,757–247,897undeterminedHD10fewer than 2 genes could be modelled
HDML122058:49,276–49,599undeterminedHD10fewer than 2 genes could be modelled
HDML122058:85,036–85,359undeterminedHD10fewer than 2 genes could be modelled
HDML122071:274,991–311,887undeterminedHD1, HD20fewer than 2 genes could be modelled
HDML122053:115,365–118,301undeterminedHD20fewer than 2 genes could be modelled
HDML122053:475,386–480,570undeterminedHD10fewer than 2 genes could be modelled
HDML122048:802,608–802,739undeterminedHD20fewer than 2 genes could be modelled
HDML122048:1,525,534–1,525,641undeterminedHD20fewer than 2 genes could be modelled
HDML122101:61,883–62,017undeterminedHD20fewer than 2 genes could be modelled
HDML122074:7,021–24,829undeterminedHD20fewer than 2 genes could be modelled
PRML122065:309,196–318,059undeterminedpheromone_receptor, fungal_mating_type_pheromone0fewer than 2 genes could be modelled
HDML122118:11,743–18,476undeterminedHD10fewer than 2 genes could be modelled
PRML122045:1,231,124–1,241,249undeterminedpheromone_receptor, pheromone_B430fewer than 2 genes could be modelled
HDML122051:1,075,564–1,075,701undeterminedHD10fewer than 2 genes could be modelled
HDML122046:349,367–349,564undeterminedHD20fewer than 2 genes could be modelled
HDML122046:382,778–383,212undeterminedHD20fewer than 2 genes could be modelled
HDML122046:1,895,731–1,911,248undeterminedHD20fewer than 2 genes could be modelled
PRML122054:138,636–143,496undeterminedpheromone_receptor, fungal_mating_type_pheromone0fewer than 2 genes could be modelled
HDML122080:280,857–281,027undeterminedHD20fewer than 2 genes could be modelled
HDML122050:560,923–561,513undeterminedHD20fewer than 2 genes could be modelled
HDML122050:620,006–620,467undeterminedHD10fewer than 2 genes could be modelled
HDML122093:61,098–61,316undeterminedHD10fewer than 2 genes could be modelled
HDML122086:197,186–197,350undeterminedHD10fewer than 2 genes could be modelled
HDML122090:131,457–136,054undeterminedHD20fewer than 2 genes could be modelled
HDML122082:141,084–141,413undeterminedHD20fewer than 2 genes could be modelled
HDML122059:516,767–516,925undeterminedHD20fewer than 2 genes could be modelled
HDML122105:100,174–100,392undeterminedHD20fewer than 2 genes could be modelled
HDML122132:3,611–3,772undeterminedHD20fewer than 2 genes could be modelled
HDML122083:151,724–151,843undeterminedHD20fewer than 2 genes could be modelled
HDML122095:67,839–68,030undeterminedHD20fewer than 2 genes could be modelled
HDML122061:188,409–188,600undeterminedHD10fewer than 2 genes could be modelled
HDML122070:3,473–3,625undeterminedHD10fewer than 2 genes could be modelled
HDML122070:28,807–29,064undeterminedHD10fewer than 2 genes could be modelled
HDML122072:278,763–278,870undeterminedHD10fewer than 2 genes could be modelled
HDML122062:187,358–205,660undeterminedHD20fewer than 2 genes could be modelled
HDML122088:21,131–21,268undeterminedHD20fewer than 2 genes could be modelled
PRML122043:2,601,203–2,606,296undeterminedpheromone_receptor, caax_precursor1too few of the family's genes found
PRML122047:503,331–509,012undeterminedpheromone_receptor, caax_precursor1too few of the family's genes found
PRML122049:486,093–497,520undeterminedfungal_mating_type_pheromone1too few of the family's genes found

Provenance

Genome file
LtigrinusALCF2SS1-7.genome.fasta
Assembly
207 contigs · 39.5 Mb · N50 846.1 kb
Genome SHA-256
4d5a68fb5096a311a162e94a31c7bed5266ebb5763b920fb5fc4a611c8f8a15f
MATPredict
0.8.1 (v0.8.1, 3a62e6302b)
Database
86f18d232e4fe95d · 185 records
Taxonomy
local NCBI taxonomy snapshot 2026-10-01
Parameters
phylum=Basidiomycota, phylum_guess={'requested': 'auto', 'status': 'ok', 'usable': True, 'reason': None, 'phylum': 'Basidiomycota', 'phylum_taxid': 5204, 'deepest_rank': 'species', 'routing_taxid': 5317, '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 Basidiomycota', 'action': 'routed', 'weak_call_accepted': False, 'genetic_code': 1, 'genetic_code_from': 'family taxid 5317', 'routed_by': 'family taxid 5317 (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
2026-11-07T02:10:00Z
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