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
MC265843 40 52.42 2.9 0.01 20.18 20.41 0.0 PF08550 94.59 29.26 Shifted
MC265850 32 109.03 4.07 0.03 0.0 1.85 0.0 UNKNOWN 0.0 0.0 NONE
MC265861 27 233.48 16.74 0.07 0.0 0.59 4.22 UNKNOWN 0.0 0.0 NONE
MC265921 30 198.97 15.54 0.02 0.0 0.02 0.0 UNKNOWN 0.0 0.0 NONE
MC265965 29 207.14 16.08 0.03 0.0 0.0 0.0 UNKNOWN 0.0 0.0 NONE
MC265978 49 169.53 19.18 0.02 0.0 0.42 0.09 PF00646 36.96 20.3 Extended
MC265995 25 81.88 3.37 0.02 0.0 3.57 0.0 PF13407 95.0 13.58 Shifted
MC266112 25 144.84 12.33 0.05 31.02 59.46 0.0 UNKNOWN 0.0 0.0 NONE
MC266137 28 196.11 29.49 0.09 0.0 26.28 0.0 UNKNOWN 0.0 0.0 NONE
MC266173 25 54.96 4.0 0.06 0.0 5.74 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.