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
MC287468 153 59.67 4.68 0.84 0.0 7.07 0.03 PF03065 99.26 20.2 Reduced
MC287469 45 127.31 10.85 0.09 0.0 10.42 0.2 UNKNOWN 0.0 0.0 NONE
MC287472 249 102.59 21.3 9.69 1.11 29.46 0.0 PF18876 93.08 47.65 Reduced
MC287476 69 185.03 22.14 19.32 5.81 65.38 0.0 PF06758 25.64 30.33 Extended
MC287499 27 85.56 9.62 0.01 0.0 0.91 0.0 PF01761 52.38 3.0 Shifted
MC287501 57 134.19 19.3 3.04 19.3 38.43 0.0 UNKNOWN 0.0 0.0 NONE
MC287509 3683 80.69 7.23 0.77 0.06 8.99 0.0 PF07776 94.77 90.2 Equivalent
MC287524 46 143.26 7.32 0.03 0.0 0.11 0.0 PF10730 100.0 99.59 Equivalent
MC287548 83 777.14 80.91 10.68 0.0 69.99 0.0 PF00642 1.23 2.55 Extended
MC287554 334 375.81 42.5 4.05 0.0 22.41 0.02 PF10009 96.34 91.01 Equivalent
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.