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
MC486068 33 416.82 41.63 0.08 1.66 83.71 0.0 UNKNOWN 0.0 0.0 NONE
MC486077 142 91.54 18.07 1.19 0.19 19.69 0.05 PF17919 0.7 4.32 Shifted
MC486081 66 181.47 30.27 1.31 0.0 23.02 0.04 PF04473 2.38 44.2 Extended
MC486097 29 110.38 8.33 0.01 0.0 0.06 0.0 PF16285 100.0 45.57 Reduced
MC486099 439 94.97 12.03 1.34 0.0 21.91 0.0 PF03143 54.52 93.51 Equivalent
MC486103 33 321.09 55.22 0.05 0.0 3.04 0.0 UNKNOWN 0.0 0.0 NONE
MC486108 349 308.4 44.4 3.46 0.1 15.04 0.06 UNKNOWN 0.0 0.0 NONE
MC486126 178 62.08 6.15 1.65 0.0 13.16 0.0 PF00135 96.32 18.05 Reduced
MC486158 120 335.19 37.2 1.82 0.33 27.64 0.0 UNKNOWN 0.0 0.0 NONE
MC486160 945 87.24 8.48 1.97 0.19 25.4 0.0 PF00004 1.04 12.02 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.