MATPredict · mating-type report

CalbicansSC5314

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 02:31 UTC by MATPredict 0.8.1

Result

Mating type

Ahigh confidence

Called loci 1

A MTL family · Ascomycota

high confidence
Gene order of the A locus on Ca22chr5A_C_albicans_SC5314A locus: genes from left to right on Ca22chr5A_C_albicans_SC5314, 393,493 to 402,144: MTLA1 (core MAT gene, minus strand); MTLA2 (core MAT gene, minus strand); PIK1 (variable flank, minus strand); OBP1 (variable flank, minus strand); PAP1 (variable flank, plus strand).394 kb396 kb398 kb400 kb402 kb← 393.1 kb more to contig endcalled locusMTLA1: core MAT gene, 393,493–394,455 (-), identity 99.5%, search hit onlyMTLA1MTLA2: core MAT gene, 394,560–395,220 (-), identity 100.0%, search hit onlyMTLA2PIK1: variable flank, 395,335–398,205 (-), identity 100.0%, search hit onlyPIK1OBP1: variable flank, 398,770–400,071 (-), identity 100.0%, search hit onlyOBP1PAP1: variable flank, 400,477–402,144 (+), identity 100.0%, search hit onlyPAP1
Gene order on Ca22chr5A_C_albicans_SC5314. Scroll sideways to see the whole figure.
FungiDB release 71 gene models on Ca22chr5A_C_albicans_SC5314, 393,061 to 402,576C5_01730W_A 390,706-393,267 (+): Ortholog of C. dubliniensis CD36 : Cd36_51590, C. parapsilosis CDC317 : CPAR2_303610, C. auris B8441 : B9J08_001456 and Candida tenuis NRRL Y-1498 : CANTEDRAFT_135127C5_01730W_AC5_01740C_A 393,493-394,455 (-): Homeodomain protein of the MTLa mating type locus, a1 and alpha2 together repress white-opaque switching and mating (an opaque-specific process), a/alpha mating type may increase virulence by competitive advantage, Spider biofilm inducedC5_01740C_A MTLA1C5_01750C_A 394,560-395,220 (-): Master regulator (activator) of a-type mating, has HMG domain, which is predicted to bind DNA, gene has intron, not related to S. cerevisiae MATa2, a/alpha mating type may increase virulence, provides competitive advantageC5_01750C_A MTLA2C5_01760C_A 395,335-398,205 (-): Phosphatidylinositol 4-kinase, controls levels of phosphatidylinositol-4-phosphate (PI(4)P) in the Golgi, non-sex gene located in MTLa mating-type-like locus, nonidentical gene encoding PI(4)P kinase, PIKALPHA, located in MTLalpha locusC5_01760C_A PIKAC5_01770C_A 398,770-400,071 (-): Similar to oxysterol binding protein, non-sex gene located within the MTLa mating-type-like locus, Plc1p-regulatedC5_01770C_A OBPAC5_01780W_A 400,477-402,144 (+): Poly(A) polymerase, likely involved in mRNA polyadenylation, PAP is inhibited by parnafungin antifungals, non-sex gene located within the MTLa mating-type-like locusC5_01780W_A PAP1C5_01790C_A 402,452-402,754 (-): Ortholog of Candida albicans WO-1 : CAWG_04564C5_01790C_A
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
  • variable flank
  • search hit only
Location
Ca22chr5A_C_albicans_SC5314:393,493–402,144 · 8.7 kb
Cross-lineage class
MAT1-2
Own genes
Ca22chr5A_C_albicans_SC5314:393,493–402,144 · 8.7 kb
Locus
Complete locus: MAT gene(s) with their flanking genes.
Genes modelled
5 of 5 gene hits
Nearest contig end
393.5 kb
Region (samtools)
Ca22chr5A_C_albicans_SC5314:393493-402144
Idiomorph scores
  • A 386.0

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
MTLA1core MAThit onlyDIAMOND, proteome99.5cov 100.0%1.0e-137376 bits393,493–394,455 -–5476_sc5314_MTL_AC5_01740C_A MTLA1
MTLA2core MAThit onlyDIAMOND, proteome100.0cov 100.0%5.6e-142386 bits394,560–395,220 -–5476_sc5314_MTL_AC5_01750C_A MTLA2
PIK1variable flankhit onlyDIAMOND, proteome100.0cov 100.0%< 1e-1801,822 bits395,335–398,205 -–5476_sc5314_MTL_AC5_01760C_A PIKA
OBP1variable flankhit onlyDIAMOND, proteome100.0cov 100.0%2.9e-315844 bits398,770–400,071 -–5476_sc5314_MTL_AC5_01770C_A OBPA
PAP1variable flankhit onlyDIAMOND, proteome100.0cov 100.0%< 1e-1801,102 bits400,477–402,144 +–5476_sc5314_MTL_AC5_01780W_A PAP1

Withheld candidate loci 27

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

Show the 27 withheld loci

Withheld loci (27)

familylocationidiomorph genesmodelledreason
MTLCa22chr1A_C_albicans_SC5314:483,219–483,491AMTLA10fewer than 2 genes could be modelled
MTLCa22chr1A_C_albicans_SC5314:757,339–757,497AMTLA20fewer than 2 genes could be modelled
MTLCa22chr1A_C_albicans_SC5314:1,739,369–1,739,512AMTLA10fewer than 2 genes could be modelled
MTLCa22chr1A_C_albicans_SC5314:2,458,246–2,460,650alphaMTLA1, MTLalpha10fewer than 2 genes could be modelled
MTLCa22chr1A_C_albicans_SC5314:2,551,893–2,552,027alphaMTLalpha10fewer than 2 genes could be modelled
MTLCa22chr1A_C_albicans_SC5314:2,748,560–2,748,928AMTLA10fewer than 2 genes could be modelled
MTLCa22chr5A_C_albicans_SC5314:1,119,139–1,119,309AMTLA10fewer than 2 genes could be modelled
MTLCa22chrRA_C_albicans_SC5314:261,995–262,102AMTLA10fewer than 2 genes could be modelled
MTLCa22chrRA_C_albicans_SC5314:686,754–686,891alphaMTLalpha10fewer than 2 genes could be modelled
MTLCa22chrRA_C_albicans_SC5314:757,465–772,119AMTLA20fewer than 2 genes could be modelled
MTLCa22chrRA_C_albicans_SC5314:821,489–821,608AMTLA20fewer than 2 genes could be modelled
MTLCa22chrRA_C_albicans_SC5314:909,556–909,711AMTLA10fewer than 2 genes could be modelled
MTLCa22chrRA_C_albicans_SC5314:1,873,612–1,873,770alphaMTLalpha10fewer than 2 genes could be modelled
MTLCa22chrRA_C_albicans_SC5314:2,096,035–2,096,151AMTLA10fewer than 2 genes could be modelled
MTLCa22chr6A_C_albicans_SC5314:131,196–131,483alphaMTLalpha10fewer than 2 genes could be modelled
MTLCa22chr6A_C_albicans_SC5314:740,455–740,562alphaMTLalpha10fewer than 2 genes could be modelled
MTLCa22chr3A_C_albicans_SC5314:120,380–120,520alphaMTLalpha10fewer than 2 genes could be modelled
MTLCa22chr3A_C_albicans_SC5314:724,085–724,180alphaMTLalpha10fewer than 2 genes could be modelled
MTLCa22chr3A_C_albicans_SC5314:840,136–840,237AMTLA10fewer than 2 genes could be modelled
MTLCa22chr2A_C_albicans_SC5314:1,306,734–1,306,850alphaMTLalpha10fewer than 2 genes could be modelled
MTLCa22chr7A_C_albicans_SC5314:205,339–205,545AMTLA10fewer than 2 genes could be modelled
MTLCa22chr4A_C_albicans_SC5314:121,577–121,675alphaMTLalpha10fewer than 2 genes could be modelled
MTLCa22chr4A_C_albicans_SC5314:790,070–790,222AMTLA20fewer than 2 genes could be modelled
MTLCa22chr4A_C_albicans_SC5314:955,393–955,575AMTLA10fewer than 2 genes could be modelled
MTLCa22chr1A_C_albicans_SC5314:1,427,895–1,430,957undeterminedPIK11too few of the family's genes found
MTLCa22chrRA_C_albicans_SC5314:1,006,481–1,008,139undeterminedOBP11too few of the family's genes found
MTLCa22chrRA_C_albicans_SC5314:1,540,034–1,545,817undeterminedPIK11too few of the family's genes found

Provenance

Genome file
CalbicansSC5314.genome.fasta
Assembly
9 contigs · 14.3 Mb · N50 2.2 Mb
Genome SHA-256
8fff7094a50808bec2696fdf9c4e5558f06d17c6218b1d3030ff228444d6e092
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': 'genus', 'routing_taxid': 766764, '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': 12, 'genetic_code_from': 'family taxid 766764', 'routed_by': 'family taxid 766764 (lineage)'}, genetic_code=12, 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
2026-11-07T02:31:19Z
Run time
25 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