MATPredict · mating-type report

CparapsilosisCDC317

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 02:21 UTC by MATPredict 0.8.1

Result

Mating type

Amedium confidence

Called loci 1

A MTL family · Ascomycota

medium confidence
Gene order of the A locus on Contig005806_C_parapsilosis_CDC317A locus: genes from left to right on Contig005806_C_parapsilosis_CDC317, 830,236 to 838,733: PAP1 (variable flank, minus strand); OBP1 (variable flank, plus strand); PIK1 (variable flank, plus strand); MTLA2 (core MAT gene, plus strand); MTLA1 (core MAT gene, plus strand).830 kb832 kb834 kb836 kb838 kb200.6 kb more to contig end →called locusPAP1: variable flank, 830,236–831,894 (-), identity 74.0%, search hit onlyPAP1OBP1: variable flank, 832,251–833,570 (+), identity 66.4%, search hit onlyOBP1PIK1: variable flank, 833,828–836,641 (+), identity 65.0%, search hit onlyPIK1MTLA2: core MAT gene, 837,296–837,953 (+), identity 43.0%, search hit onlyMTLA2MTLA1: core MAT gene, 838,335–838,733 (+), identity 31.111%, search hit onlyMTLA1
Gene order on Contig005806_C_parapsilosis_CDC317. Scroll sideways to see the whole figure.
FungiDB release 71 gene models on Contig005806_C_parapsilosis_CDC317, 829,812 to 839,157CPAR2_303550 828,504-830,207 (+): Has domain(s) with predicted amino acid transmembrane transporter activity, role in amino acid transmembrane transport, amino acid transport, transmembrane transport and integral component of membrane, membrane localizationCPAR2_303550 HIP1CPAR2_303560 830,236-831,894 (-): Ortholog(s) have RNA adenylyltransferase activity, polynucleotide adenylyltransferase activity and role in mRNA polyadenylation, nuclear-transcribed mRNA catabolic process, meiosis-specific transcripts, sno(s)RNA polyadenylationCPAR2_303560CPAR2_303570 832,251-833,570 (+): Ortholog(s) have lipid binding, sterol transfer activityCPAR2_303570CPAR2_303580 833,828-836,641 (+): Ortholog(s) have 1-phosphatidylinositol 4-kinase activity, role in phosphatidylinositol phosphorylation, positive regulation of autophagosome assembly and nucleus, trans-Golgi network localizationCPAR2_303580CPAR2_303590 837,296-837,953 (+): Ortholog of C. albicans SC5314 : C5_01750C_A/MTLA2, Debaryomyces hansenii CBS767 : DEHA2E19140g, Candida metapsilosis : CMET_43 and Pichia stipitis Pignal : PICST_33462CPAR2_303590CPAR2_303600 838,071-838,739 (+): unspecified productCPAR2_303600CPAR2_303610 839,041-841,212 (-): Ortholog of C. albicans SC5314 : C5_01730W_A, C. dubliniensis CD36 : Cd36_51590, C. auris B8441 : B9J08_001456 and Candida tenuis NRRL Y-1498 : CANTEDRAFT_135127CPAR2_303610
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
Contig005806_C_parapsilosis_CDC317:830,236–838,733 · 8.5 kb
Cross-lineage class
MAT1-2
Own genes
Contig005806_C_parapsilosis_CDC317:830,236–838,733 · 8.5 kb
Locus
Complete locus: MAT gene(s) with their flanking genes.
Genes modelled
4 of 5 gene hits
Nearest contig end
201.0 kb
Region (samtools)
Contig005806_C_parapsilosis_CDC317:830236-838733
Idiomorph scores
  • A 140.0

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
PAP1variable flankhit onlyDIAMOND, proteome74.0cov 99.6%3.8e-310841 bits830,236–831,894 -–5476_sc5314_MTL_ACPAR2_303560
OBP1variable flankhit onlyDIAMOND, proteome66.4cov 99.3%2.5e-204563 bits832,251–833,570 +–5476_sc5314_MTL_ACPAR2_303570
PIK1variable flankhit onlyDIAMOND, proteome65.0cov 99.4%< 1e-1801,127 bits833,828–836,641 +–5476_sc5314_MTL_ACPAR2_303580
MTLA2core MAThit onlyDIAMOND, proteome43.0cov 99.0%9.7e-45140 bits837,296–837,953 +–5476_sc5314_MTL_ACPAR2_303590
MTLA1core MAThit onlytblastn31.1cov 53.0%2.0e-0750 bits838,335–838,733 +–5476_sc5314_MTL_ACPAR2_303600

Withheld candidate loci 37

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 (35); too few of the family's genes found (2).

Show the 37 withheld loci

Withheld loci (37)

familylocationidiomorph genesmodelledreason
MTLContig005809_C_parapsilosis_CDC317:560,652–560,999AMTLA10fewer than 2 genes could be modelled
MTLContig005809_C_parapsilosis_CDC317:1,941,280–1,941,438alphaMTLalpha10fewer than 2 genes could be modelled
MTLContig005809_C_parapsilosis_CDC317:2,007,905–2,050,024alphaMTLA2, MTLalpha1, OBP11fewer than 2 genes could be modelled
MTLContig005809_C_parapsilosis_CDC317:2,275,576–2,275,707AMTLA20fewer than 2 genes could be modelled
MTLContig005806_C_parapsilosis_CDC317:50,822–51,031AMTLA10fewer than 2 genes could be modelled
MTLContig005806_C_parapsilosis_CDC317:988,971–989,171AMTLA20fewer than 2 genes could be modelled
MTLContig006110_C_parapsilosis_CDC317:123,121–128,229alphaMTLA1, MTLalpha10fewer than 2 genes could be modelled
MTLContig006110_C_parapsilosis_CDC317:585,723–585,932AMTLA10fewer than 2 genes could be modelled
MTLContig005569_C_parapsilosis_CDC317:389,722–389,829AMTLA10fewer than 2 genes could be modelled
MTLContig005569_C_parapsilosis_CDC317:445,497–445,757AMTLA20fewer than 2 genes could be modelled
MTLContig005569_C_parapsilosis_CDC317:553,355–553,516AMTLA20fewer than 2 genes could be modelled
MTLContig005569_C_parapsilosis_CDC317:613,032–637,266alphaMTLalpha10fewer than 2 genes could be modelled
MTLContig005569_C_parapsilosis_CDC317:981,759–981,863AMTLA20fewer than 2 genes could be modelled
MTLContig005569_C_parapsilosis_CDC317:1,007,587–1,007,703alphaMTLalpha10fewer than 2 genes could be modelled
MTLContig005569_C_parapsilosis_CDC317:1,113,238–1,116,306alphaMTLA1, MTLalpha10fewer than 2 genes could be modelled
MTLContig005569_C_parapsilosis_CDC317:1,785,585–1,785,800AMTLA10fewer than 2 genes could be modelled
MTLContig005807_C_parapsilosis_CDC317:197,831–198,016AMTLA20fewer than 2 genes could be modelled
MTLContig005807_C_parapsilosis_CDC317:534,940–535,191AMTLA10fewer than 2 genes could be modelled
MTLContig005807_C_parapsilosis_CDC317:585,477–585,572alphaMTLalpha10fewer than 2 genes could be modelled
MTLContig005807_C_parapsilosis_CDC317:769,280–769,411AMTLA10fewer than 2 genes could be modelled
MTLContig005807_C_parapsilosis_CDC317:910,580–910,810AMTLA20fewer than 2 genes could be modelled
MTLContig005807_C_parapsilosis_CDC317:1,123,585–1,123,695AMTLA20fewer than 2 genes could be modelled
MTLContig005807_C_parapsilosis_CDC317:1,164,087–1,164,203AMTLA20fewer than 2 genes could be modelled
MTLContig005807_C_parapsilosis_CDC317:1,627,680–1,627,817AMTLA20fewer than 2 genes could be modelled
MTLContig006139_C_parapsilosis_CDC317:617,037–617,357AMTLA10fewer than 2 genes could be modelled
MTLContig006139_C_parapsilosis_CDC317:774,486–774,644AMTLA20fewer than 2 genes could be modelled
MTLContig006372_C_parapsilosis_CDC317:214,664–214,828AMTLA10fewer than 2 genes could be modelled
MTLContig006372_C_parapsilosis_CDC317:330,768–330,878AMTLA10fewer than 2 genes could be modelled
MTLContig006372_C_parapsilosis_CDC317:443,494–443,613AMTLA20fewer than 2 genes could be modelled
MTLContig006372_C_parapsilosis_CDC317:594,153–594,716AMTLA20fewer than 2 genes could be modelled
MTLContig006372_C_parapsilosis_CDC317:860,787–860,894AMTLA20fewer than 2 genes could be modelled
MTLContig006372_C_parapsilosis_CDC317:911,249–911,467alphaMTLalpha10fewer than 2 genes could be modelled
MTLContig006372_C_parapsilosis_CDC317:1,008,977–1,009,102AMTLA20fewer than 2 genes could be modelled
MTLContig006372_C_parapsilosis_CDC317:1,532,286–1,535,945AMTLA10fewer than 2 genes could be modelled
MTLContig006372_C_parapsilosis_CDC317:1,772,530–1,772,682AMTLA20fewer than 2 genes could be modelled
MTLContig005809_C_parapsilosis_CDC317:872,401–878,154undeterminedPIK11too few of the family's genes found
MTLContig005809_C_parapsilosis_CDC317:1,464,897–1,468,130undeterminedPIK11too few of the family's genes found

Provenance

Genome file
CparapsilosisCDC317.genome.fasta
Assembly
9 contigs · 13.0 Mb · N50 2.1 Mb
Genome SHA-256
e6d18299e160deff97adb9184e2047324c63dc08e33fc8f4b903e1f808683d96
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': 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
2026-11-07T02:20:43Z
Run time
22 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