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
MC34639 52 105.33 17.96 2.61 0.0 54.77 0.0 PF12885 100.0 36.51 Shifted
MC34640 88 190.58 29.42 10.29 0.0 4.02 3.52 PF01594 75.71 60.22 Reduced
MC34641 39 536.13 72.27 0.03 0.07 0.44 3.97 UNKNOWN 0.0 0.0 NONE
MC34644 262 139.15 19.52 2.32 0.15 15.56 0.01 PF04840 99.15 55.96 Reduced
MC34648 34 191.26 13.0 0.02 0.0 8.83 0.0 UNKNOWN 0.0 0.0 NONE
MC34652 41 193.78 12.76 0.02 0.0 0.54 0.0 UNKNOWN 0.0 0.0 NONE
MC34660 26 60.54 3.73 0.03 0.0 3.31 0.0 UNKNOWN 0.0 0.0 NONE
MC34661 85 287.73 50.45 1.34 0.0 22.36 0.0 PF09648 1.64 56.5 Extended
MC34663 53 86.21 10.27 11.89 0.66 59.55 0.0 PF08528 100.0 26.91 Extended
MC34665 57 98.72 10.25 2.7 0.0 22.32 0.05 PF15056 100.0 82.93 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.