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
MC460418 64 273.56 37.29 1.83 0.0 19.1 0.09 UNKNOWN 0.0 0.0 NONE
MC460439 48 781.04 112.18 0.02 0.51 0.93 0.3 PF02985 20.0 3.15 Extended
MC460458 38 73.42 6.93 0.03 0.0 0.65 0.0 PF14516 42.11 16.24 Shifted
MC460459 5261 134.56 18.38 2.05 0.0 31.04 0.0 PF00754 82.1 85.1 Equivalent
MC460468 187 90.5 5.95 1.51 0.0 30.01 0.0 PF02211 99.25 62.36 Reduced
MC460473 6420 79.28 12.68 2.35 0.0 22.52 0.0 PF07859 98.09 35.05 Reduced
MC460518 193 147.0 15.23 12.39 0.0 0.88 4.45 PF06496 100.0 91.06 Equivalent
MC460532 48 64.12 6.29 0.04 0.0 13.23 0.0 PF13646 2.63 81.82 Equivalent
MC460533 130 81.85 9.45 1.15 0.0 16.29 0.0 PF17903 98.21 65.28 Extended
MC460535 542 133.56 19.61 2.52 10.08 18.19 0.0 PF01485 1.06 0.93 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.