Evolution & Discovery

Explore the PWWP family.

Domain sequences, evolutionary relationships and the evidence behind them. Follow a domain from alignment to its experimental structures.

Literature & timeline

AnalysisPWWP-EVO-1.0.0

Domain sequences—

Alignment sites retained—

Evolutionary model—

Domain-level analysis

Relationships with support in view.

Unrooted analysis

Analysis representation

Aligned tracks

Protein scale

Support labels Constructs

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All rows share the same tree geometry. Select an internal branch to inspect its support, reorder its children or collapse its displayed tips.

39 analyzed domain tips

Figure mode

SH-aLRT ≥80 & UFBoot ≥95Lower / unavailable supportAlignment-sensitiveObserved domain coordinatesNo observed core in snapshot

Drag to pan · Scroll or use + / − to zoom · Select a label to inspect its evidence. The drawing origin is arbitrary; it is not an inferred ancestor.

Accessible domain list and search results

From sequences to residues

Inspect the alignment.

Download the exact data ↓

Conservation is descriptive of the sampled sequences. Gaps and excluded positions remain visible; conservation alone does not assign binding function.

Rows

Columns

Start column

Window

Literal PWWP motifSource-supported cageDeposited ligand proximityExcluded alignment site

PWWP is the naming motif, not an invariant sequence. Variant motifs occur in validated family members; absence of the literal tetrapeptide does not exclude the fold.

Residue evidence

Choose an aligned residue.

Each position maps back to the canonical UniProt sequence. Structure and comparison links are available only where recorded evidence supports them.

Scope of the analysis

Candidates and unresolved boundaries.

Predicted PWWP-like candidates are shown separately. Annotation-supported domains can also be excluded when their folded-domain boundaries or alignment coverage do not meet the analysis criteria.

Reproducible analysis

Methods, sources & downloads.

New analysis · frozen dataset v1.2

Analysis record

Interpretation limits

Support-collapsed unrooted cladogram; branch lengths omittedpwwp_supported_splits.nwk Primary unrooted maximum-likelihood treepwwp_unrooted_ml.nwk Full MAFFT L-INS-i alignment (gaps and excluded columns retained)alignment_linsi.fasta Qualified inference alignmentalignment_masked.fasta Exact canonical domain-interval sequencesdomain_sequences.fasta Exact full canonical Atlas sequencescanonical_sequences.fasta Source and analysis domain boundariesdomain_boundaries.tsv Every alignment position and exclusion reasonalignment_columns.tsv Alignment-to-canonical residue mapalignment_residue_mapping.tsv Broader-mask sensitivity treepwwp_sensitivity_ml.nwk MAFFT E-INS-i sensitivity alignmentalignment_einsi.fasta Structure correspondence diagnosticstructure_alignment_diagnostic.tsv Pairwise sequence identity over shared retained sitespairwise_sequence_similarity.tsv Branch support and sensitivitybranch_support.json Comparison with published2012 relationshipspublished_relationship_comparison.json Assessment of all nine nonhuman comparatorsnonhuman_sampling_assessment.json Published sequences mapped to current canonical boundssource_boundary_validation.json Complete primary IQ-TREE inference reportiqtree_primary_report.txt Complete sensitivity IQ-TREE inference reportiqtree_sensitivity_report.txt Exact executable parameters and software environmentrun_environment.json Scientific results, limits and manuscript assessmentRESULTS.md Exact scientific methods and limitationsMETHODS.md

Phase 5 sampling and inference diagnostics

The tree and architecture presentation follows the linked-view principle of Storm & Sonnhammer, NIFAS (2001). Display operations change no topology, support calculation, sequence or annotation coordinate.

Source provenance and boundary decisions

Open the complete machine-readable analysis and linked evidence

The interactive tree and alignment require JavaScript.

The exact sequence files, methods and tree are available in the downloads above. The original protein and domain records remain accessible without JavaScript.