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
MC15984 1167 401.13 30.68 2.13 0.0 12.78 0.09 PF01973 99.19 41.66 Extended
MC15989 58 88.19 7.87 1.42 0.5 13.3 0.0 PF05157 95.56 71.81 Extended
MC15990 76 133.65 8.54 2.16 5.07 19.21 0.0 PF09055 95.45 92.51 Equivalent
MC15993 332 92.17 6.65 1.28 0.0 15.75 0.06 PF10351 99.66 29.08 Reduced
MC15995 63 521.21 44.03 4.3 2.93 13.22 0.07 PF03704 58.93 6.91 Shifted
MC15997 66 56.55 3.16 3.16 0.0 19.68 0.0 PF05582 100.0 22.32 Reduced
MC15999 241 134.63 34.07 7.54 0.0 59.21 0.05 PF10248 93.62 78.75 Equivalent
MC16000 66 137.74 13.51 1.77 0.0 9.42 0.71 PF00149 73.08 13.29 Shifted
MC16026 104 74.35 4.56 1.25 13.8 28.99 0.0 UNKNOWN 0.0 0.0 NONE
MC16045 52 961.4 154.12 4.57 0.32 26.15 0.1 PF12366-PF12366 52.08 76.43 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.