Kinase Motif Triad

Audit the ordered VAIK, HRD, and DFG kinase-domain motifs.

Description

An ordered kinase-motif screen checks three exact segments and their sequence order.

An ordered kinase-motif screen checks three exact segments and their sequence order. The first occurrence of each segment controls the result.^[1]

Audit the ordered VAIK, HRD, and DFG kinase-domain motifs.

When to use Kinase Motif Triad

Use this tool to audit the ordered VAIK, HRD, and DFG kinase-domain motifs.

Prepare the canonical sequence, peptide assignments, fitted assay parameters or upstream measurements requested. Keep corresponding entries aligned, use the stated mass and signal units, and remove FASTA headers before entering sequence text.

How to use Kinase Motif Triad and understand its results

Prepare the canonical sequence, peptide assignments, fitted assay parameters or upstream measurements requested. Keep corresponding entries aligned, use the stated mass and signal units, and remove FASTA headers before entering sequence text.
Enter sequence using the field table and calculation rules, then run the tool.
Read motifPositions, triadOrdered. The explanation below defines the units, signs, ordering and any flags or placeholder values.
If the tool reports an input issue, correct the values and run it again. Apply the stated assumptions when interpreting a successfully returned result.

Input field	Meaning	Value type; see rules below	Requirement
sequence	Sequence	string	Required

Enter a canonical sequence. Return three zero-based positions in VAIK/HRD/DFG order, using −1 for absent segments, and the strict ordered flag.

The shared sequence helper trims outer whitespace and uppercases the sequence. It requires at least one residue from ACDEFGHIKLMNPQRSTVWY. Internal whitespace, FASTA headers, ambiguous letters and modified-residue notation are rejected. Sequence indexes refer to the normalized sequence; individual tools may preserve original strings in their returned lists as explained above.

positions=[indexOf(VAIK),indexOf(HRD),indexOf(DFG)]; ordered=0≤p0<p1<p2

Units, indexing, boundary conditions and exceptional cases are defined in the calculation rules above.

Output field	Meaning	Value type
motifPositions	Motif positions	list of number
triadOrdered	Triad ordered	boolean

json

{
  "input": {
    "sequence": "VAIKAAHRDAADFG"
  },
  "output": {
    "motifPositions": [
      0,
      6,
      11
    ],
    "triadOrdered": true
  }
}

Limitations and assumptions

Alternative motif variants and later occurrences are not searched for a better ordered triad. Domain identity, spacing and catalytic activity are not assessed.

Numeric inputs must be finite. Follow the calculation-specific rules for overflow, underflow and exceptional cases. Extremely large text inputs are rejected. Missing required fields, extra fields, wrong value types and violations of the calculation rules are input errors. A successfully returned false flag is an evaluated outcome; its meaning is explained above.

Alternative or Complementary methods

Use Walker A Motifs: Find Walker A/P-loop nucleotide-binding consensus candidates. For a complementary task, use SH2 Flvres Motif: Check an SH2-domain sequence for a FLVRES-like phosphotyrosine-binding motif.

References

Kinase Motif Triad — tool.io

Similar or alternative tools

Walker A Motifs
Find Walker A/P-loop nucleotide-binding consensus candidates.
SH2 Flvres Motif
Check an SH2-domain sequence for a FLVRES-like phosphotyrosine-binding motif.