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
MC499345 2582 126.02 30.34 2.29 0.0 23.57 0.01 PF07603 72.7 87.77 Equivalent
MC499348 108 78.05 8.41 1.08 0.0 2.47 0.67 UNKNOWN 0.0 0.0 NONE
MC499371 185 69.91 7.25 19.4 0.0 8.11 1.94 PF10745 86.01 84.65 Equivalent
MC499372 293 459.2 84.8 2.47 0.03 19.69 0.0 PF13387 99.55 38.11 Extended
MC499374 95 111.01 17.91 11.99 0.0 40.81 0.0 PF05142 98.67 30.81 Shifted
MC499376 152 133.03 18.91 4.5 0.0 17.08 0.03 PF00780 82.61 4.14 Shifted
MC499378 621 70.03 5.21 1.59 0.0 20.64 0.0 PF00133 99.82 15.79 Reduced
MC499414 66 64.52 10.12 23.05 0.0 11.83 0.94 UNKNOWN 0.0 0.0 NONE
MC499447 71 66.41 4.9 0.0 0.0 23.4 0.0 UNKNOWN 0.0 0.0 NONE
MC499452 329 2349.21 486.57 2.23 0.01 20.82 0.36 PF12340-PF12359 65.71 14.3 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.