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
MC373217 151 202.95 22.96 3.11 0.0 13.45 0.01 PF01861 99.22 85.03 Equivalent
MC373223 84 69.5 9.62 1.23 0.0 44.58 0.0 PF15244 97.73 32.22 Reduced
MC373226 108 209.5 34.52 16.71 1.14 61.8 0.0 UNKNOWN 0.0 0.0 NONE
MC373264 106 236.51 25.55 4.47 1.22 23.97 0.02 UNKNOWN 0.0 0.0 NONE
MC373271 115 104.56 23.62 11.51 0.0 33.4 0.0 UNKNOWN 0.0 0.0 NONE
MC373298 51 68.24 7.38 4.31 0.0 22.27 0.0 PF09700 10.0 37.3 Reduced
MC373316 105 60.94 5.54 0.0 0.0 35.29 0.0 PF00400 21.51 48.58 Extended
MC373343 80 135.59 5.77 1.39 0.0 14.37 0.0 UNKNOWN 0.0 0.0 NONE
MC373352 77 67.96 10.71 2.38 0.0 23.67 0.0 PF02190 93.94 37.64 Reduced
MC373375 74 62.34 9.51 0.7 0.0 11.43 0.03 PF16134 85.71 22.79 Reduced
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.