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
MC203173 1401 95.93 15.69 1.6 0.0 32.83 0.0 PF00630 71.2 83.81 Equivalent
MC203174 98 112.91 16.35 8.46 34.58 55.04 0.0 PF15035 15.79 13.44 Shifted
MC203175 118 81.47 8.89 0.58 0.0 48.61 0.0 PF02847 1.35 55.86 Reduced
MC203181 237 67.4 4.72 0.13 0.0 21.88 0.0 PF07992 71.43 11.28 Shifted
MC203182 58 237.0 18.71 1.56 0.0 16.46 0.04 UNKNOWN 0.0 0.0 NONE
MC203186 32 69.53 8.31 0.49 0.0 91.24 0.0 PF09738 100.0 22.25 Shifted
MC203187 101 514.29 56.8 4.01 0.07 16.82 0.07 PF05664 80.0 81.81 Equivalent
MC203193 29 110.97 5.96 0.0 0.0 2.39 0.0 UNKNOWN 0.0 0.0 NONE
MC203201 39 86.97 11.87 0.07 0.0 27.86 0.0 PF07228 18.42 11.13 Shifted
MC203204 87 93.99 8.9 5.13 0.0 11.34 0.0 PF16727 98.33 86.43 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.