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
MC13423 52 344.54 25.44 11.41 0.0 30.87 0.0 PF09663 93.75 99.07 Equivalent
MC13427 29 128.52 14.69 0.01 0.0 3.11 0.14 UNKNOWN 0.0 0.0 NONE
MC13429 35 288.37 9.14 0.03 0.0 3.36 0.0 PF14478 95.65 23.81 Extended
MC13433 25 51.56 4.14 0.0 0.0 19.94 0.0 UNKNOWN 0.0 0.0 NONE
MC13438 48 548.5 67.07 0.05 0.0 35.93 0.0 PF12859 100.0 22.87 Extended
MC13449 27 148.78 11.94 0.04 0.0 1.59 1.95 UNKNOWN 0.0 0.0 NONE
MC13454 98 67.11 9.45 0.72 0.0 32.64 0.0 PF02498 82.61 41.28 Shifted
MC13455 36 161.94 13.35 0.05 0.0 1.18 0.0 PF13482 91.18 7.09 Shifted
MC13456 79 81.37 10.12 1.48 0.0 8.72 0.0 UNKNOWN 0.0 0.0 NONE
MC13460 172 84.1 8.98 0.36 0.26 9.23 0.04 PF00535 10.0 4.67 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.