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
MC173330 42 63.0 7.08 0.26 3.89 10.32 0.06 UNKNOWN 0.0 0.0 NONE
MC173402 26 91.27 10.26 0.0 0.0 4.93 0.0 UNKNOWN 0.0 0.0 NONE
MC173408 41 123.71 10.52 0.08 1.47 0.0 3.38 UNKNOWN 0.0 0.0 NONE
MC173419 43 118.65 12.33 0.03 0.0 1.06 0.0 PF01094 75.68 43.38 Reduced
MC173443 43 790.44 107.02 0.08 0.0 80.65 0.0 UNKNOWN 0.0 0.0 NONE
MC173446 25 81.72 5.36 0.01 0.0 13.08 0.0 PF07040 90.91 34.22 Shifted
MC173447 27 117.93 11.28 0.12 3.73 11.59 0.0 UNKNOWN 0.0 0.0 NONE
MC173469 26 314.73 38.75 0.08 0.0 40.85 0.0 UNKNOWN 0.0 0.0 NONE
MC173489 41 845.76 150.54 0.17 0.12 74.58 0.0 PF15273 10.0 35.14 Extended
MC173497 45 51.64 7.0 0.0 0.0 1.04 0.0 PF10118 68.75 12.47 Shifted
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.