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
MC387875 32 61.59 8.44 0.02 0.0 0.61 0.0 PF17194 100.0 61.91 Reduced
MC387885 30 170.63 20.3 0.03 0.0 13.38 0.4 PF00069-PF00656 66.67 41.44 Reduced
MC387889 587 57.05 6.43 2.32 0.0 18.8 0.01 PF00579 99.07 11.7 Shifted
MC387890 741 422.15 61.13 4.91 0.93 22.5 0.06 PF00221 93.46 95.6 Equivalent
MC387892 140 182.35 22.11 1.84 0.0 21.49 0.01 UNKNOWN 0.0 0.0 NONE
MC387895 227 148.18 20.43 2.57 13.15 24.27 0.04 UNKNOWN 0.0 0.0 NONE
MC387896 87 119.79 16.79 0.46 0.0 21.13 0.0 PF13597 92.96 27.82 Reduced
MC387909 78 144.37 15.85 4.44 0.0 14.81 0.0 UNKNOWN 0.0 0.0 NONE
MC387916 355 85.62 14.88 2.2 0.0 19.27 0.01 PF00586-PF02769 81.42 31.75 Reduced
MC387932 36 131.0 13.28 0.01 0.0 17.41 0.0 PF07004 21.74 15.8 Extended
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.