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
MC398069 78 68.64 5.83 0.38 0.0 11.71 0.0 PF00855 100.0 52.59 Shifted
MC398088 86 113.69 19.52 3.78 0.0 29.18 0.0 PF04852 82.81 84.38 Equivalent
MC398099 31 78.0 7.3 0.05 0.0 3.44 0.47 PF00899 59.26 28.28 Reduced
MC398106 79 51.67 6.08 2.54 0.0 2.5 1.3 PF09685 17.57 41.27 Shifted
MC398116 427 73.63 8.08 1.56 0.0 20.25 0.0 PF08441 96.89 24.02 Reduced
MC398119 32 123.94 20.13 0.03 0.0 3.78 0.1 PF03708 38.46 12.71 Shifted
MC398130 232 152.72 19.95 3.52 0.0 6.14 0.09 PF04925 96.53 86.57 Equivalent
MC398133 2850 334.67 52.37 4.22 1.19 22.64 0.02 PF02181 93.39 90.11 Equivalent
MC398140 222 165.69 20.66 1.17 0.0 16.92 0.0 PF17116 100.0 52.99 Reduced
MC398151 349 200.04 21.24 1.77 2.16 14.33 0.02 PF02259 0.6 0.96 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.