DPCfam Metaclusters

🧬 Domain Classification in Sequence Space
DPCfam Standard DPCfam DPCfamB

The DPCfam pipeline applied the Density Peak Clustering (DPC) algorithm to roughly 23 million UniRef50 sequences (UniRef50 v. 2017_07) and automatically grouped homologous domain segments into 81,384 protein families called metaclusters, entirely without manual curation. Each metacluster was then used to build a multiple sequence alignment and a profile-HMM for downstream analysis.

The table below lists all 81,384 DPCfam metaclusters by default. Use the toggle buttons above to switch to the Standard subset (size ≥ 50 seeds, 46,828 metaclusters) or the DPCfamB subset (25 to 49 seeds, 34,556 metaclusters). Intrinsic metacluster properties appear on the left; Pfam annotations on the right. Click any MCID to open its detail page.

MCID Size UniRef50 Avg. Len. Std avg len % LC % CC % DIS Avg. TM Pfam DA % DA % Avg. Ov. Overlap Label
MC419336 140 78.86 5.52 12.96 0.0 8.02 1.94 UNKNOWN 0.0 0.0 NONE
MC419337 2137 59.56 4.92 3.03 0.02 6.72 0.03 PF04991 89.39 33.64 Shifted
MC419342 37 145.03 12.84 0.11 0.0 71.28 0.0 UNKNOWN 0.0 0.0 NONE
MC419346 93 82.18 10.43 2.02 0.0 29.7 0.03 UNKNOWN 0.0 0.0 NONE
MC419348 515 107.7 13.87 6.77 0.21 3.45 1.86 PF11750 94.56 92.76 Equivalent
MC419355 221 242.34 33.27 2.75 5.4 16.61 0.04 PF14631 91.86 58.03 Reduced
MC419358 62 85.6 7.53 14.35 0.0 3.22 1.74 UNKNOWN 0.0 0.0 NONE
MC419371 364 246.54 33.48 6.24 0.02 10.7 0.31 PF14429 1.42 34.54 Shifted
MC419373 1029 91.36 12.26 3.61 0.0 28.34 0.02 PF01795 98.85 35.36 Reduced
MC419378 25 90.48 7.05 0.0 0.0 7.12 0.0 PF01156 100.0 33.08 Reduced
Legend
  • A. Metacluster Intrinsic Properties:
  • MCID: Unique identifier per metacluster.
  • 1. Size UniRef50 : Number of UniRef50 seed sequences in the metacluster.
  • 2. Avg. Len.: Mean domain length of the seeds (in amino acids).
  • 3. Std. Avg. Len.: Standard deviation of seed domain lengths.
  • 4. % LC Percent of residues located in low-complexity regions.
  • 5. % CC: Percent of residues located in coiled-coil regions.
  • 6. % DIS: Percent of residues predicted as intrinsically disordered.
  • 7. Avg.TM: Average number of transmembrane regions per domain.
  • B. Pfam Annotations:
  • 1. Pfam DA: Pfam architecture which best overlaps with MC. We refer to it as the dominant architecture (DA). If there is no overlap, the MC is tagged as UNKNOWN (representing 'dark matter').
  • 2. % DA: Percent of sequences in the MC matching the DA.
  • 3. % Avg. Ov.: Average % boundary overlap between the MC and Pfam, computed only for seeds that match the DA.
  • 4. Overlap Label: Label describing qualitatively the overlap of the MC with its DA, which can be : equivalent, reduced, extended or shifted. NONE, otherwise.
    Color-coded based on boundary agreement:
    • Yellow (Equivalent): the MC and its dominant architecture share very similar boundaries.
    • Blue (Reduced): the MC covers only part of the dominant architecture.
    • Pink (Extended): the MC extends beyond the dominant architecture boundaries.
    • Green (Shifted): the MC and the dominant architecture share a boundary offset, with poor positional agreement.