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
MC349589 60 146.47 23.83 0.74 0.0 23.78 0.0 PF18470 28.89 17.55 Shifted
MC349603 127 128.84 19.89 8.7 0.1 26.84 0.0 PF00612 16.19 14.96 Extended
MC349617 70 73.89 6.62 2.79 0.0 31.12 0.0 UNKNOWN 0.0 0.0 NONE
MC349656 65 331.02 36.39 3.32 0.0 23.67 0.02 UNKNOWN 0.0 0.0 NONE
MC349686 355 338.07 68.23 9.51 0.0 42.6 0.0 PF05920 48.13 5.67 Shifted
MC349692 44 290.09 41.16 0.07 0.0 35.52 0.0 PF10383 84.21 62.46 Extended
MC349693 63 60.6 3.79 0.0 0.0 37.37 0.0 PF00102 91.11 5.46 Shifted
MC349704 45 458.0 69.6 0.09 0.0 16.79 0.0 UNKNOWN 0.0 0.0 NONE
MC349708 76 306.8 27.94 6.65 0.0 25.72 0.0 UNKNOWN 0.0 0.0 NONE
MC349713 27 266.93 46.58 0.01 0.61 1.97 0.0 UNKNOWN 0.0 0.0 NONE
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.