C2H2 Zinc Finger Motifs

Find C2H2 zinc-finger cysteine/histidine spacing patterns.

Description

A C2H2 zinc-finger sequence screen locates candidates with a particular residue pattern.

A C2H2 zinc-finger sequence screen locates candidates with a particular residue pattern. Pattern presence is a starting point for examining biological context and experimental evidence.^[1]

Find C2H2 zinc-finger cysteine/histidine spacing patterns.

When to use C2H2 Zinc Finger Motifs

Use this tool to find C2H2 zinc-finger cysteine/histidine spacing patterns.

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 C2H2 Zinc Finger Motifs 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 motifStarts, motifCount. 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 the canonical sequence. Examine each possible start for C-X(2–4)-C-X(12)-H-X(3–4)-H, implemented by C.{2,4}C.{12}H.{3,4}H. X means any accepted amino acid. Return zero-based start positions and their count in ascending order; overlapping matches are retained. Variable spacing is accepted within the stated bounds.

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.

match pattern: C-X(2–4)-C-X(12)-H-X(3–4)-H; count=number of matching start positions

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

Output field	Meaning	Value type
motifStarts	Motif starts	list of number
motifCount	Motif count	number

json

{
  "input": {
    "sequence": "CAACAAAAAAAAAAAAHAAAH"
  },
  "output": {
    "motifStarts": [
      0
    ],
    "motifCount": 1
  }
}

Limitations and assumptions

The scan is limited to this exact pattern. It does not confirm C2H2 zinc-finger function, structural accessibility or experimental support.

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.

Alternative or Complementary methods

Use Ef Hand Loop Screen: Screen predicted EF-hand loops by length and acidic-residue count. For a complementary task, use Kinase Motif Triad: Audit the ordered VAIK, HRD, and DFG kinase-domain motifs.

References

C2H2 Zinc Finger Motifs — tool.io

Similar or alternative tools

Ef Hand Loop Screen
Screen predicted EF-hand loops by length and acidic-residue count.
Kinase Motif Triad
Audit the ordered VAIK, HRD, and DFG kinase-domain motifs.